RPTRF: A rapid perfect tandem repeat finder tool for DNA sequences
The sequencing of eukaryotic genomes has shown that tandem repeats are abundant in their sequences. In addition to affecting some cellular processes, tandem repeats in the genome may be associated with specific diseases and have been the key to resolving criminal cases. Any tool developed for detect...
Ausführliche Beschreibung
Autor*in: |
Behboudi, Reza [verfasserIn] Nouri-Baygi, Mostafa [verfasserIn] Naghibzadeh, Mahmoud [verfasserIn] |
---|
Format: |
E-Artikel |
---|---|
Sprache: |
Englisch |
Erschienen: |
2023 |
---|
Schlagwörter: |
---|
Übergeordnetes Werk: |
Enthalten in: Biosystems - Amsterdam [u.a.] : Elsevier Science, 1967, 226 |
---|---|
Übergeordnetes Werk: |
volume:226 |
DOI / URN: |
10.1016/j.biosystems.2023.104869 |
---|
Katalog-ID: |
ELV009530118 |
---|
LEADER | 01000caa a22002652 4500 | ||
---|---|---|---|
001 | ELV009530118 | ||
003 | DE-627 | ||
005 | 20230926162231.0 | ||
007 | cr uuu---uuuuu | ||
008 | 230511s2023 xx |||||o 00| ||eng c | ||
024 | 7 | |a 10.1016/j.biosystems.2023.104869 |2 doi | |
035 | |a (DE-627)ELV009530118 | ||
035 | |a (ELSEVIER)S0303-2647(23)00044-8 | ||
040 | |a DE-627 |b ger |c DE-627 |e rda | ||
041 | |a eng | ||
082 | 0 | 4 | |a 570 |q VZ |
084 | |a BIODIV |q DE-30 |2 fid | ||
084 | |a 44.00 |2 bkl | ||
100 | 1 | |a Behboudi, Reza |e verfasserin |4 aut | |
245 | 1 | 0 | |a RPTRF: A rapid perfect tandem repeat finder tool for DNA sequences |
264 | 1 | |c 2023 | |
336 | |a nicht spezifiziert |b zzz |2 rdacontent | ||
337 | |a Computermedien |b c |2 rdamedia | ||
338 | |a Online-Ressource |b cr |2 rdacarrier | ||
520 | |a The sequencing of eukaryotic genomes has shown that tandem repeats are abundant in their sequences. In addition to affecting some cellular processes, tandem repeats in the genome may be associated with specific diseases and have been the key to resolving criminal cases. Any tool developed for detecting tandem repeats must be accurate, fast, and useable in thousands of laboratories worldwide, including those with not very advanced computing capabilities. The proposed method, the Rapid Perfect Tandem Repeat Finder (RPTRF), minimizes the need for excess character comparison processing by indexing the input file and significantly helps to accelerate and prepare the output without artifacts by using an interval tree in the filtering section. The experiments demonstrated that the RPTRF is very fast in discovering all perfect tandem repeats of all categories of any genomic sequences. Although the detection of imperfect TRs is not the focus of the RPTRF, comparisons show that it even outperforms some other tools (in five selected gold standards) designed explicitly for this purpose. | ||
650 | 4 | |a Consecutive tandem repeats | |
650 | 4 | |a Perfect tandem repeats | |
650 | 4 | |a Genomic sequences | |
700 | 1 | |a Nouri-Baygi, Mostafa |e verfasserin |4 aut | |
700 | 1 | |a Naghibzadeh, Mahmoud |e verfasserin |4 aut | |
773 | 0 | 8 | |i Enthalten in |t Biosystems |d Amsterdam [u.a.] : Elsevier Science, 1967 |g 226 |h Online-Ressource |w (DE-627)306320843 |w (DE-600)1496359-0 |w (DE-576)081952953 |7 nnns |
773 | 1 | 8 | |g volume:226 |
912 | |a GBV_USEFLAG_U | ||
912 | |a GBV_ELV | ||
912 | |a SYSFLAG_U | ||
912 | |a FID-BIODIV | ||
912 | |a SSG-OLC-PHA | ||
912 | |a GBV_ILN_20 | ||
912 | |a GBV_ILN_22 | ||
912 | |a GBV_ILN_23 | ||
912 | |a GBV_ILN_24 | ||
912 | |a GBV_ILN_31 | ||
912 | |a GBV_ILN_32 | ||
912 | |a GBV_ILN_40 | ||
912 | |a GBV_ILN_60 | ||
912 | |a GBV_ILN_62 | ||
912 | |a GBV_ILN_65 | ||
912 | |a GBV_ILN_69 | ||
912 | |a GBV_ILN_70 | ||
912 | |a GBV_ILN_73 | ||
912 | |a GBV_ILN_74 | ||
912 | |a GBV_ILN_90 | ||
912 | |a GBV_ILN_95 | ||
912 | |a GBV_ILN_100 | ||
912 | |a GBV_ILN_101 | ||
912 | |a GBV_ILN_105 | ||
912 | |a GBV_ILN_110 | ||
912 | |a GBV_ILN_150 | ||
912 | |a GBV_ILN_151 | ||
912 | |a GBV_ILN_187 | ||
912 | |a GBV_ILN_213 | ||
912 | |a GBV_ILN_224 | ||
912 | |a GBV_ILN_230 | ||
912 | |a GBV_ILN_370 | ||
912 | |a GBV_ILN_602 | ||
912 | |a GBV_ILN_702 | ||
912 | |a GBV_ILN_2001 | ||
912 | |a GBV_ILN_2003 | ||
912 | |a GBV_ILN_2004 | ||
912 | |a GBV_ILN_2005 | ||
912 | |a GBV_ILN_2007 | ||
912 | |a GBV_ILN_2008 | ||
912 | |a GBV_ILN_2009 | ||
912 | |a GBV_ILN_2010 | ||
912 | |a GBV_ILN_2011 | ||
912 | |a GBV_ILN_2014 | ||
912 | |a GBV_ILN_2015 | ||
912 | |a GBV_ILN_2020 | ||
912 | |a GBV_ILN_2021 | ||
912 | |a GBV_ILN_2025 | ||
912 | |a GBV_ILN_2026 | ||
912 | |a GBV_ILN_2027 | ||
912 | |a GBV_ILN_2034 | ||
912 | |a GBV_ILN_2044 | ||
912 | |a GBV_ILN_2048 | ||
912 | |a GBV_ILN_2049 | ||
912 | |a GBV_ILN_2050 | ||
912 | |a GBV_ILN_2055 | ||
912 | |a GBV_ILN_2056 | ||
912 | |a GBV_ILN_2059 | ||
912 | |a GBV_ILN_2061 | ||
912 | |a GBV_ILN_2064 | ||
912 | |a GBV_ILN_2088 | ||
912 | |a GBV_ILN_2106 | ||
912 | |a GBV_ILN_2110 | ||
912 | |a GBV_ILN_2111 | ||
912 | |a GBV_ILN_2112 | ||
912 | |a GBV_ILN_2122 | ||
912 | |a GBV_ILN_2129 | ||
912 | |a GBV_ILN_2143 | ||
912 | |a GBV_ILN_2152 | ||
912 | |a GBV_ILN_2153 | ||
912 | |a GBV_ILN_2190 | ||
912 | |a GBV_ILN_2232 | ||
912 | |a GBV_ILN_2336 | ||
912 | |a GBV_ILN_2470 | ||
912 | |a GBV_ILN_2507 | ||
912 | |a GBV_ILN_4035 | ||
912 | |a GBV_ILN_4037 | ||
912 | |a GBV_ILN_4112 | ||
912 | |a GBV_ILN_4125 | ||
912 | |a GBV_ILN_4242 | ||
912 | |a GBV_ILN_4249 | ||
912 | |a GBV_ILN_4251 | ||
912 | |a GBV_ILN_4305 | ||
912 | |a GBV_ILN_4306 | ||
912 | |a GBV_ILN_4307 | ||
912 | |a GBV_ILN_4313 | ||
912 | |a GBV_ILN_4322 | ||
912 | |a GBV_ILN_4323 | ||
912 | |a GBV_ILN_4324 | ||
912 | |a GBV_ILN_4325 | ||
912 | |a GBV_ILN_4326 | ||
912 | |a GBV_ILN_4333 | ||
912 | |a GBV_ILN_4334 | ||
912 | |a GBV_ILN_4338 | ||
912 | |a GBV_ILN_4393 | ||
912 | |a GBV_ILN_4700 | ||
936 | b | k | |a 44.00 |j Medizin: Allgemeines |q VZ |
951 | |a AR | ||
952 | |d 226 |
author_variant |
r b rb m n b mnb m n mn |
---|---|
matchkey_str |
behboudirezanouribaygimostafanaghibzadeh:2023----:praaipretadmeetidro |
hierarchy_sort_str |
2023 |
bklnumber |
44.00 |
publishDate |
2023 |
allfields |
10.1016/j.biosystems.2023.104869 doi (DE-627)ELV009530118 (ELSEVIER)S0303-2647(23)00044-8 DE-627 ger DE-627 rda eng 570 VZ BIODIV DE-30 fid 44.00 bkl Behboudi, Reza verfasserin aut RPTRF: A rapid perfect tandem repeat finder tool for DNA sequences 2023 nicht spezifiziert zzz rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The sequencing of eukaryotic genomes has shown that tandem repeats are abundant in their sequences. In addition to affecting some cellular processes, tandem repeats in the genome may be associated with specific diseases and have been the key to resolving criminal cases. Any tool developed for detecting tandem repeats must be accurate, fast, and useable in thousands of laboratories worldwide, including those with not very advanced computing capabilities. The proposed method, the Rapid Perfect Tandem Repeat Finder (RPTRF), minimizes the need for excess character comparison processing by indexing the input file and significantly helps to accelerate and prepare the output without artifacts by using an interval tree in the filtering section. The experiments demonstrated that the RPTRF is very fast in discovering all perfect tandem repeats of all categories of any genomic sequences. Although the detection of imperfect TRs is not the focus of the RPTRF, comparisons show that it even outperforms some other tools (in five selected gold standards) designed explicitly for this purpose. Consecutive tandem repeats Perfect tandem repeats Genomic sequences Nouri-Baygi, Mostafa verfasserin aut Naghibzadeh, Mahmoud verfasserin aut Enthalten in Biosystems Amsterdam [u.a.] : Elsevier Science, 1967 226 Online-Ressource (DE-627)306320843 (DE-600)1496359-0 (DE-576)081952953 nnns volume:226 GBV_USEFLAG_U GBV_ELV SYSFLAG_U FID-BIODIV SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_150 GBV_ILN_151 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 44.00 Medizin: Allgemeines VZ AR 226 |
spelling |
10.1016/j.biosystems.2023.104869 doi (DE-627)ELV009530118 (ELSEVIER)S0303-2647(23)00044-8 DE-627 ger DE-627 rda eng 570 VZ BIODIV DE-30 fid 44.00 bkl Behboudi, Reza verfasserin aut RPTRF: A rapid perfect tandem repeat finder tool for DNA sequences 2023 nicht spezifiziert zzz rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The sequencing of eukaryotic genomes has shown that tandem repeats are abundant in their sequences. In addition to affecting some cellular processes, tandem repeats in the genome may be associated with specific diseases and have been the key to resolving criminal cases. Any tool developed for detecting tandem repeats must be accurate, fast, and useable in thousands of laboratories worldwide, including those with not very advanced computing capabilities. The proposed method, the Rapid Perfect Tandem Repeat Finder (RPTRF), minimizes the need for excess character comparison processing by indexing the input file and significantly helps to accelerate and prepare the output without artifacts by using an interval tree in the filtering section. The experiments demonstrated that the RPTRF is very fast in discovering all perfect tandem repeats of all categories of any genomic sequences. Although the detection of imperfect TRs is not the focus of the RPTRF, comparisons show that it even outperforms some other tools (in five selected gold standards) designed explicitly for this purpose. Consecutive tandem repeats Perfect tandem repeats Genomic sequences Nouri-Baygi, Mostafa verfasserin aut Naghibzadeh, Mahmoud verfasserin aut Enthalten in Biosystems Amsterdam [u.a.] : Elsevier Science, 1967 226 Online-Ressource (DE-627)306320843 (DE-600)1496359-0 (DE-576)081952953 nnns volume:226 GBV_USEFLAG_U GBV_ELV SYSFLAG_U FID-BIODIV SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_150 GBV_ILN_151 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 44.00 Medizin: Allgemeines VZ AR 226 |
allfields_unstemmed |
10.1016/j.biosystems.2023.104869 doi (DE-627)ELV009530118 (ELSEVIER)S0303-2647(23)00044-8 DE-627 ger DE-627 rda eng 570 VZ BIODIV DE-30 fid 44.00 bkl Behboudi, Reza verfasserin aut RPTRF: A rapid perfect tandem repeat finder tool for DNA sequences 2023 nicht spezifiziert zzz rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The sequencing of eukaryotic genomes has shown that tandem repeats are abundant in their sequences. In addition to affecting some cellular processes, tandem repeats in the genome may be associated with specific diseases and have been the key to resolving criminal cases. Any tool developed for detecting tandem repeats must be accurate, fast, and useable in thousands of laboratories worldwide, including those with not very advanced computing capabilities. The proposed method, the Rapid Perfect Tandem Repeat Finder (RPTRF), minimizes the need for excess character comparison processing by indexing the input file and significantly helps to accelerate and prepare the output without artifacts by using an interval tree in the filtering section. The experiments demonstrated that the RPTRF is very fast in discovering all perfect tandem repeats of all categories of any genomic sequences. Although the detection of imperfect TRs is not the focus of the RPTRF, comparisons show that it even outperforms some other tools (in five selected gold standards) designed explicitly for this purpose. Consecutive tandem repeats Perfect tandem repeats Genomic sequences Nouri-Baygi, Mostafa verfasserin aut Naghibzadeh, Mahmoud verfasserin aut Enthalten in Biosystems Amsterdam [u.a.] : Elsevier Science, 1967 226 Online-Ressource (DE-627)306320843 (DE-600)1496359-0 (DE-576)081952953 nnns volume:226 GBV_USEFLAG_U GBV_ELV SYSFLAG_U FID-BIODIV SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_150 GBV_ILN_151 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 44.00 Medizin: Allgemeines VZ AR 226 |
allfieldsGer |
10.1016/j.biosystems.2023.104869 doi (DE-627)ELV009530118 (ELSEVIER)S0303-2647(23)00044-8 DE-627 ger DE-627 rda eng 570 VZ BIODIV DE-30 fid 44.00 bkl Behboudi, Reza verfasserin aut RPTRF: A rapid perfect tandem repeat finder tool for DNA sequences 2023 nicht spezifiziert zzz rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The sequencing of eukaryotic genomes has shown that tandem repeats are abundant in their sequences. In addition to affecting some cellular processes, tandem repeats in the genome may be associated with specific diseases and have been the key to resolving criminal cases. Any tool developed for detecting tandem repeats must be accurate, fast, and useable in thousands of laboratories worldwide, including those with not very advanced computing capabilities. The proposed method, the Rapid Perfect Tandem Repeat Finder (RPTRF), minimizes the need for excess character comparison processing by indexing the input file and significantly helps to accelerate and prepare the output without artifacts by using an interval tree in the filtering section. The experiments demonstrated that the RPTRF is very fast in discovering all perfect tandem repeats of all categories of any genomic sequences. Although the detection of imperfect TRs is not the focus of the RPTRF, comparisons show that it even outperforms some other tools (in five selected gold standards) designed explicitly for this purpose. Consecutive tandem repeats Perfect tandem repeats Genomic sequences Nouri-Baygi, Mostafa verfasserin aut Naghibzadeh, Mahmoud verfasserin aut Enthalten in Biosystems Amsterdam [u.a.] : Elsevier Science, 1967 226 Online-Ressource (DE-627)306320843 (DE-600)1496359-0 (DE-576)081952953 nnns volume:226 GBV_USEFLAG_U GBV_ELV SYSFLAG_U FID-BIODIV SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_150 GBV_ILN_151 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 44.00 Medizin: Allgemeines VZ AR 226 |
allfieldsSound |
10.1016/j.biosystems.2023.104869 doi (DE-627)ELV009530118 (ELSEVIER)S0303-2647(23)00044-8 DE-627 ger DE-627 rda eng 570 VZ BIODIV DE-30 fid 44.00 bkl Behboudi, Reza verfasserin aut RPTRF: A rapid perfect tandem repeat finder tool for DNA sequences 2023 nicht spezifiziert zzz rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The sequencing of eukaryotic genomes has shown that tandem repeats are abundant in their sequences. In addition to affecting some cellular processes, tandem repeats in the genome may be associated with specific diseases and have been the key to resolving criminal cases. Any tool developed for detecting tandem repeats must be accurate, fast, and useable in thousands of laboratories worldwide, including those with not very advanced computing capabilities. The proposed method, the Rapid Perfect Tandem Repeat Finder (RPTRF), minimizes the need for excess character comparison processing by indexing the input file and significantly helps to accelerate and prepare the output without artifacts by using an interval tree in the filtering section. The experiments demonstrated that the RPTRF is very fast in discovering all perfect tandem repeats of all categories of any genomic sequences. Although the detection of imperfect TRs is not the focus of the RPTRF, comparisons show that it even outperforms some other tools (in five selected gold standards) designed explicitly for this purpose. Consecutive tandem repeats Perfect tandem repeats Genomic sequences Nouri-Baygi, Mostafa verfasserin aut Naghibzadeh, Mahmoud verfasserin aut Enthalten in Biosystems Amsterdam [u.a.] : Elsevier Science, 1967 226 Online-Ressource (DE-627)306320843 (DE-600)1496359-0 (DE-576)081952953 nnns volume:226 GBV_USEFLAG_U GBV_ELV SYSFLAG_U FID-BIODIV SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_150 GBV_ILN_151 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 44.00 Medizin: Allgemeines VZ AR 226 |
language |
English |
source |
Enthalten in Biosystems 226 volume:226 |
sourceStr |
Enthalten in Biosystems 226 volume:226 |
format_phy_str_mv |
Article |
bklname |
Medizin: Allgemeines |
institution |
findex.gbv.de |
topic_facet |
Consecutive tandem repeats Perfect tandem repeats Genomic sequences |
dewey-raw |
570 |
isfreeaccess_bool |
false |
container_title |
Biosystems |
authorswithroles_txt_mv |
Behboudi, Reza @@aut@@ Nouri-Baygi, Mostafa @@aut@@ Naghibzadeh, Mahmoud @@aut@@ |
publishDateDaySort_date |
2023-01-01T00:00:00Z |
hierarchy_top_id |
306320843 |
dewey-sort |
3570 |
id |
ELV009530118 |
language_de |
englisch |
fullrecord |
<?xml version="1.0" encoding="UTF-8"?><collection xmlns="http://www.loc.gov/MARC21/slim"><record><leader>01000caa a22002652 4500</leader><controlfield tag="001">ELV009530118</controlfield><controlfield tag="003">DE-627</controlfield><controlfield tag="005">20230926162231.0</controlfield><controlfield tag="007">cr uuu---uuuuu</controlfield><controlfield tag="008">230511s2023 xx |||||o 00| ||eng c</controlfield><datafield tag="024" ind1="7" ind2=" "><subfield code="a">10.1016/j.biosystems.2023.104869</subfield><subfield code="2">doi</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-627)ELV009530118</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(ELSEVIER)S0303-2647(23)00044-8</subfield></datafield><datafield tag="040" ind1=" " ind2=" "><subfield code="a">DE-627</subfield><subfield code="b">ger</subfield><subfield code="c">DE-627</subfield><subfield code="e">rda</subfield></datafield><datafield tag="041" ind1=" " ind2=" "><subfield code="a">eng</subfield></datafield><datafield tag="082" ind1="0" ind2="4"><subfield code="a">570</subfield><subfield code="q">VZ</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">BIODIV</subfield><subfield code="q">DE-30</subfield><subfield code="2">fid</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">44.00</subfield><subfield code="2">bkl</subfield></datafield><datafield tag="100" ind1="1" ind2=" "><subfield code="a">Behboudi, Reza</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">RPTRF: A rapid perfect tandem repeat finder tool for DNA sequences</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="c">2023</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="a">nicht spezifiziert</subfield><subfield code="b">zzz</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="a">Computermedien</subfield><subfield code="b">c</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="a">Online-Ressource</subfield><subfield code="b">cr</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="520" ind1=" " ind2=" "><subfield code="a">The sequencing of eukaryotic genomes has shown that tandem repeats are abundant in their sequences. In addition to affecting some cellular processes, tandem repeats in the genome may be associated with specific diseases and have been the key to resolving criminal cases. Any tool developed for detecting tandem repeats must be accurate, fast, and useable in thousands of laboratories worldwide, including those with not very advanced computing capabilities. The proposed method, the Rapid Perfect Tandem Repeat Finder (RPTRF), minimizes the need for excess character comparison processing by indexing the input file and significantly helps to accelerate and prepare the output without artifacts by using an interval tree in the filtering section. The experiments demonstrated that the RPTRF is very fast in discovering all perfect tandem repeats of all categories of any genomic sequences. Although the detection of imperfect TRs is not the focus of the RPTRF, comparisons show that it even outperforms some other tools (in five selected gold standards) designed explicitly for this purpose.</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Consecutive tandem repeats</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Perfect tandem repeats</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Genomic sequences</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Nouri-Baygi, Mostafa</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Naghibzadeh, Mahmoud</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="773" ind1="0" ind2="8"><subfield code="i">Enthalten in</subfield><subfield code="t">Biosystems</subfield><subfield code="d">Amsterdam [u.a.] : Elsevier Science, 1967</subfield><subfield code="g">226</subfield><subfield code="h">Online-Ressource</subfield><subfield code="w">(DE-627)306320843</subfield><subfield code="w">(DE-600)1496359-0</subfield><subfield code="w">(DE-576)081952953</subfield><subfield code="7">nnns</subfield></datafield><datafield tag="773" ind1="1" ind2="8"><subfield code="g">volume:226</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_USEFLAG_U</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ELV</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">SYSFLAG_U</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">FID-BIODIV</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">SSG-OLC-PHA</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_20</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_22</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_23</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_24</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_31</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_32</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_40</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_60</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_62</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_65</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_69</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_70</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_73</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_74</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_90</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_95</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_100</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_101</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_105</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_110</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_150</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_151</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_187</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_213</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_224</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_230</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_370</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_602</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_702</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2001</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2003</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2004</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2005</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2007</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2008</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2009</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2010</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2011</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2014</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2015</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2020</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2021</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2025</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2026</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2027</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2034</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2044</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2048</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2049</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2050</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2055</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2056</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2059</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2061</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2064</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2088</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2106</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2110</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2111</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2112</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2122</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2129</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2143</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2152</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2153</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2190</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2232</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2336</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2470</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2507</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4035</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4037</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4112</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4125</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4242</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4249</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4251</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4305</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4306</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4307</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4313</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4322</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4323</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4324</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4325</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4326</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4333</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4334</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4338</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4393</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4700</subfield></datafield><datafield tag="936" ind1="b" ind2="k"><subfield code="a">44.00</subfield><subfield code="j">Medizin: Allgemeines</subfield><subfield code="q">VZ</subfield></datafield><datafield tag="951" ind1=" " ind2=" "><subfield code="a">AR</subfield></datafield><datafield tag="952" ind1=" " ind2=" "><subfield code="d">226</subfield></datafield></record></collection>
|
author |
Behboudi, Reza |
spellingShingle |
Behboudi, Reza ddc 570 fid BIODIV bkl 44.00 misc Consecutive tandem repeats misc Perfect tandem repeats misc Genomic sequences RPTRF: A rapid perfect tandem repeat finder tool for DNA sequences |
authorStr |
Behboudi, Reza |
ppnlink_with_tag_str_mv |
@@773@@(DE-627)306320843 |
format |
electronic Article |
dewey-ones |
570 - Life sciences; biology |
delete_txt_mv |
keep |
author_role |
aut aut aut |
collection |
elsevier |
remote_str |
true |
illustrated |
Not Illustrated |
topic_title |
570 VZ BIODIV DE-30 fid 44.00 bkl RPTRF: A rapid perfect tandem repeat finder tool for DNA sequences Consecutive tandem repeats Perfect tandem repeats Genomic sequences |
topic |
ddc 570 fid BIODIV bkl 44.00 misc Consecutive tandem repeats misc Perfect tandem repeats misc Genomic sequences |
topic_unstemmed |
ddc 570 fid BIODIV bkl 44.00 misc Consecutive tandem repeats misc Perfect tandem repeats misc Genomic sequences |
topic_browse |
ddc 570 fid BIODIV bkl 44.00 misc Consecutive tandem repeats misc Perfect tandem repeats misc Genomic sequences |
format_facet |
Elektronische Aufsätze Aufsätze Elektronische Ressource |
format_main_str_mv |
Text Zeitschrift/Artikel |
carriertype_str_mv |
cr |
hierarchy_parent_title |
Biosystems |
hierarchy_parent_id |
306320843 |
dewey-tens |
570 - Life sciences; biology |
hierarchy_top_title |
Biosystems |
isfreeaccess_txt |
false |
familylinks_str_mv |
(DE-627)306320843 (DE-600)1496359-0 (DE-576)081952953 |
title |
RPTRF: A rapid perfect tandem repeat finder tool for DNA sequences |
ctrlnum |
(DE-627)ELV009530118 (ELSEVIER)S0303-2647(23)00044-8 |
title_full |
RPTRF: A rapid perfect tandem repeat finder tool for DNA sequences |
author_sort |
Behboudi, Reza |
journal |
Biosystems |
journalStr |
Biosystems |
lang_code |
eng |
isOA_bool |
false |
dewey-hundreds |
500 - Science |
recordtype |
marc |
publishDateSort |
2023 |
contenttype_str_mv |
zzz |
author_browse |
Behboudi, Reza Nouri-Baygi, Mostafa Naghibzadeh, Mahmoud |
container_volume |
226 |
class |
570 VZ BIODIV DE-30 fid 44.00 bkl |
format_se |
Elektronische Aufsätze |
author-letter |
Behboudi, Reza |
doi_str_mv |
10.1016/j.biosystems.2023.104869 |
dewey-full |
570 |
author2-role |
verfasserin |
title_sort |
rptrf: a rapid perfect tandem repeat finder tool for dna sequences |
title_auth |
RPTRF: A rapid perfect tandem repeat finder tool for DNA sequences |
abstract |
The sequencing of eukaryotic genomes has shown that tandem repeats are abundant in their sequences. In addition to affecting some cellular processes, tandem repeats in the genome may be associated with specific diseases and have been the key to resolving criminal cases. Any tool developed for detecting tandem repeats must be accurate, fast, and useable in thousands of laboratories worldwide, including those with not very advanced computing capabilities. The proposed method, the Rapid Perfect Tandem Repeat Finder (RPTRF), minimizes the need for excess character comparison processing by indexing the input file and significantly helps to accelerate and prepare the output without artifacts by using an interval tree in the filtering section. The experiments demonstrated that the RPTRF is very fast in discovering all perfect tandem repeats of all categories of any genomic sequences. Although the detection of imperfect TRs is not the focus of the RPTRF, comparisons show that it even outperforms some other tools (in five selected gold standards) designed explicitly for this purpose. |
abstractGer |
The sequencing of eukaryotic genomes has shown that tandem repeats are abundant in their sequences. In addition to affecting some cellular processes, tandem repeats in the genome may be associated with specific diseases and have been the key to resolving criminal cases. Any tool developed for detecting tandem repeats must be accurate, fast, and useable in thousands of laboratories worldwide, including those with not very advanced computing capabilities. The proposed method, the Rapid Perfect Tandem Repeat Finder (RPTRF), minimizes the need for excess character comparison processing by indexing the input file and significantly helps to accelerate and prepare the output without artifacts by using an interval tree in the filtering section. The experiments demonstrated that the RPTRF is very fast in discovering all perfect tandem repeats of all categories of any genomic sequences. Although the detection of imperfect TRs is not the focus of the RPTRF, comparisons show that it even outperforms some other tools (in five selected gold standards) designed explicitly for this purpose. |
abstract_unstemmed |
The sequencing of eukaryotic genomes has shown that tandem repeats are abundant in their sequences. In addition to affecting some cellular processes, tandem repeats in the genome may be associated with specific diseases and have been the key to resolving criminal cases. Any tool developed for detecting tandem repeats must be accurate, fast, and useable in thousands of laboratories worldwide, including those with not very advanced computing capabilities. The proposed method, the Rapid Perfect Tandem Repeat Finder (RPTRF), minimizes the need for excess character comparison processing by indexing the input file and significantly helps to accelerate and prepare the output without artifacts by using an interval tree in the filtering section. The experiments demonstrated that the RPTRF is very fast in discovering all perfect tandem repeats of all categories of any genomic sequences. Although the detection of imperfect TRs is not the focus of the RPTRF, comparisons show that it even outperforms some other tools (in five selected gold standards) designed explicitly for this purpose. |
collection_details |
GBV_USEFLAG_U GBV_ELV SYSFLAG_U FID-BIODIV SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_150 GBV_ILN_151 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 |
title_short |
RPTRF: A rapid perfect tandem repeat finder tool for DNA sequences |
remote_bool |
true |
author2 |
Nouri-Baygi, Mostafa Naghibzadeh, Mahmoud |
author2Str |
Nouri-Baygi, Mostafa Naghibzadeh, Mahmoud |
ppnlink |
306320843 |
mediatype_str_mv |
c |
isOA_txt |
false |
hochschulschrift_bool |
false |
doi_str |
10.1016/j.biosystems.2023.104869 |
up_date |
2024-07-06T23:28:42.964Z |
_version_ |
1803874229777596416 |
fullrecord_marcxml |
<?xml version="1.0" encoding="UTF-8"?><collection xmlns="http://www.loc.gov/MARC21/slim"><record><leader>01000caa a22002652 4500</leader><controlfield tag="001">ELV009530118</controlfield><controlfield tag="003">DE-627</controlfield><controlfield tag="005">20230926162231.0</controlfield><controlfield tag="007">cr uuu---uuuuu</controlfield><controlfield tag="008">230511s2023 xx |||||o 00| ||eng c</controlfield><datafield tag="024" ind1="7" ind2=" "><subfield code="a">10.1016/j.biosystems.2023.104869</subfield><subfield code="2">doi</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-627)ELV009530118</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(ELSEVIER)S0303-2647(23)00044-8</subfield></datafield><datafield tag="040" ind1=" " ind2=" "><subfield code="a">DE-627</subfield><subfield code="b">ger</subfield><subfield code="c">DE-627</subfield><subfield code="e">rda</subfield></datafield><datafield tag="041" ind1=" " ind2=" "><subfield code="a">eng</subfield></datafield><datafield tag="082" ind1="0" ind2="4"><subfield code="a">570</subfield><subfield code="q">VZ</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">BIODIV</subfield><subfield code="q">DE-30</subfield><subfield code="2">fid</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">44.00</subfield><subfield code="2">bkl</subfield></datafield><datafield tag="100" ind1="1" ind2=" "><subfield code="a">Behboudi, Reza</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">RPTRF: A rapid perfect tandem repeat finder tool for DNA sequences</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="c">2023</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="a">nicht spezifiziert</subfield><subfield code="b">zzz</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="a">Computermedien</subfield><subfield code="b">c</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="a">Online-Ressource</subfield><subfield code="b">cr</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="520" ind1=" " ind2=" "><subfield code="a">The sequencing of eukaryotic genomes has shown that tandem repeats are abundant in their sequences. In addition to affecting some cellular processes, tandem repeats in the genome may be associated with specific diseases and have been the key to resolving criminal cases. Any tool developed for detecting tandem repeats must be accurate, fast, and useable in thousands of laboratories worldwide, including those with not very advanced computing capabilities. The proposed method, the Rapid Perfect Tandem Repeat Finder (RPTRF), minimizes the need for excess character comparison processing by indexing the input file and significantly helps to accelerate and prepare the output without artifacts by using an interval tree in the filtering section. The experiments demonstrated that the RPTRF is very fast in discovering all perfect tandem repeats of all categories of any genomic sequences. Although the detection of imperfect TRs is not the focus of the RPTRF, comparisons show that it even outperforms some other tools (in five selected gold standards) designed explicitly for this purpose.</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Consecutive tandem repeats</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Perfect tandem repeats</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Genomic sequences</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Nouri-Baygi, Mostafa</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Naghibzadeh, Mahmoud</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="773" ind1="0" ind2="8"><subfield code="i">Enthalten in</subfield><subfield code="t">Biosystems</subfield><subfield code="d">Amsterdam [u.a.] : Elsevier Science, 1967</subfield><subfield code="g">226</subfield><subfield code="h">Online-Ressource</subfield><subfield code="w">(DE-627)306320843</subfield><subfield code="w">(DE-600)1496359-0</subfield><subfield code="w">(DE-576)081952953</subfield><subfield code="7">nnns</subfield></datafield><datafield tag="773" ind1="1" ind2="8"><subfield code="g">volume:226</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_USEFLAG_U</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ELV</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">SYSFLAG_U</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">FID-BIODIV</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">SSG-OLC-PHA</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_20</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_22</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_23</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_24</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_31</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_32</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_40</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_60</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_62</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_65</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_69</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_70</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_73</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_74</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_90</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_95</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_100</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_101</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_105</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_110</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_150</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_151</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_187</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_213</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_224</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_230</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_370</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_602</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_702</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2001</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2003</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2004</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2005</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2007</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2008</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2009</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2010</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2011</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2014</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2015</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2020</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2021</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2025</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2026</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2027</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2034</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2044</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2048</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2049</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2050</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2055</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2056</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2059</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2061</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2064</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2088</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2106</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2110</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2111</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2112</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2122</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2129</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2143</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2152</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2153</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2190</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2232</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2336</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2470</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2507</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4035</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4037</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4112</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4125</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4242</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4249</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4251</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4305</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4306</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4307</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4313</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4322</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4323</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4324</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4325</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4326</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4333</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4334</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4338</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4393</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4700</subfield></datafield><datafield tag="936" ind1="b" ind2="k"><subfield code="a">44.00</subfield><subfield code="j">Medizin: Allgemeines</subfield><subfield code="q">VZ</subfield></datafield><datafield tag="951" ind1=" " ind2=" "><subfield code="a">AR</subfield></datafield><datafield tag="952" ind1=" " ind2=" "><subfield code="d">226</subfield></datafield></record></collection>
|
score |
7.400174 |