BOV – a web-based BLAST output visualization tool

Background The BLAST program is one of the most widely used sequence similarity search tools for genomic research, even by those biologists lacking extensive bioinformatics training. As the availability of sequence data increases, more researchers are downloading the BLAST program for local installation and performing larger and more complex tasks, including batch queries. In order to manage and interpret the results of batch queries, a host of software packages have been developed to assist with data management and post-processing. Among these programs, there is almost a complete lack of visualization tools to provide graphic representation of complex BLAST pair-wise alignments. We have developed a web-based program, B LAST O utput V isualization Tool (BOV), that allows users to interactively visualize the matching regions of query and database hit sequences, thereby allowing the user to quickly and easily dissect complex matching patterns. Results Users can upload the standard BLAST output in pair-wise alignment format as input to the web server (including batch queries generated installing and running the stand-alone BLAST program on a local server). The program extracts the alignment coordinates of matching regions between the query and the corresponding database hit sequence. The coordinates are used to plot each matching region as colored lines or trapezoids. Using the straightforward control panels throughout the web site, each plotted matching region can be easily explored in detail by, for example, highlighting the region of interest or examining the raw pair-wise sequence alignment. Tutorials are provided at the website to guide users step-by-step through the functional features of BOV. Conclusion BOV provides a user-friendly web interface to visualize the standard BLAST output for investigating wide-ranging genomic problems, including single query and batch query datasets. In particular, this software is valuable to users interested in identifying regions of co-linearity, duplication, translocation, and inversion among sequences. A web server hosting BOV is accessible via http://bioportal.cgb.indiana.edu/cgi-bin/BOV/index.cgi and the software is freely available for local installations. Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Gollapudi, Rajesh [verfasserIn] Revanna, Kashi Vishwanath Hemmerich, Chris Schaack, Sarah Dong, Qunfeng

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2008

Schlagwörter:	Blast Program Matching Region Query Region Local Installation Blast Output

Anmerkung:	© Gollapudi et al; licensee BioMed Central Ltd. 2008. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (

Übergeordnetes Werk:	Enthalten in: BMC genomics - London : BioMed Central, 2000, 9(2008), 1 vom: 15. Sept.
Übergeordnetes Werk:	volume:9 ; year:2008 ; number:1 ; day:15 ; month:09

Links:	Volltext

DOI / URN:	10.1186/1471-2164-9-414

Katalog-ID:	SPR027038041

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allfields	10.1186/1471-2164-9-414 doi (DE-627)SPR027038041 (SPR)1471-2164-9-414-e DE-627 ger DE-627 rakwb eng Gollapudi, Rajesh verfasserin aut BOV – a web-based BLAST output visualization tool 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Gollapudi et al; licensee BioMed Central Ltd. 2008. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background The BLAST program is one of the most widely used sequence similarity search tools for genomic research, even by those biologists lacking extensive bioinformatics training. As the availability of sequence data increases, more researchers are downloading the BLAST program for local installation and performing larger and more complex tasks, including batch queries. In order to manage and interpret the results of batch queries, a host of software packages have been developed to assist with data management and post-processing. Among these programs, there is almost a complete lack of visualization tools to provide graphic representation of complex BLAST pair-wise alignments. We have developed a web-based program, B LAST O utput V isualization Tool (BOV), that allows users to interactively visualize the matching regions of query and database hit sequences, thereby allowing the user to quickly and easily dissect complex matching patterns. Results Users can upload the standard BLAST output in pair-wise alignment format as input to the web server (including batch queries generated installing and running the stand-alone BLAST program on a local server). The program extracts the alignment coordinates of matching regions between the query and the corresponding database hit sequence. The coordinates are used to plot each matching region as colored lines or trapezoids. Using the straightforward control panels throughout the web site, each plotted matching region can be easily explored in detail by, for example, highlighting the region of interest or examining the raw pair-wise sequence alignment. Tutorials are provided at the website to guide users step-by-step through the functional features of BOV. Conclusion BOV provides a user-friendly web interface to visualize the standard BLAST output for investigating wide-ranging genomic problems, including single query and batch query datasets. In particular, this software is valuable to users interested in identifying regions of co-linearity, duplication, translocation, and inversion among sequences. A web server hosting BOV is accessible via http://bioportal.cgb.indiana.edu/cgi-bin/BOV/index.cgi and the software is freely available for local installations. Blast Program (dpeaa)DE-He213 Matching Region (dpeaa)DE-He213 Query Region (dpeaa)DE-He213 Local Installation (dpeaa)DE-He213 Blast Output (dpeaa)DE-He213 Revanna, Kashi Vishwanath aut Hemmerich, Chris aut Schaack, Sarah aut Dong, Qunfeng aut Enthalten in BMC genomics London : BioMed Central, 2000 9(2008), 1 vom: 15. Sept. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:9 year:2008 number:1 day:15 month:09 https://dx.doi.org/10.1186/1471-2164-9-414 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 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_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 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_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2008 1 15 09
spelling	10.1186/1471-2164-9-414 doi (DE-627)SPR027038041 (SPR)1471-2164-9-414-e DE-627 ger DE-627 rakwb eng Gollapudi, Rajesh verfasserin aut BOV – a web-based BLAST output visualization tool 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Gollapudi et al; licensee BioMed Central Ltd. 2008. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background The BLAST program is one of the most widely used sequence similarity search tools for genomic research, even by those biologists lacking extensive bioinformatics training. As the availability of sequence data increases, more researchers are downloading the BLAST program for local installation and performing larger and more complex tasks, including batch queries. In order to manage and interpret the results of batch queries, a host of software packages have been developed to assist with data management and post-processing. Among these programs, there is almost a complete lack of visualization tools to provide graphic representation of complex BLAST pair-wise alignments. We have developed a web-based program, B LAST O utput V isualization Tool (BOV), that allows users to interactively visualize the matching regions of query and database hit sequences, thereby allowing the user to quickly and easily dissect complex matching patterns. Results Users can upload the standard BLAST output in pair-wise alignment format as input to the web server (including batch queries generated installing and running the stand-alone BLAST program on a local server). The program extracts the alignment coordinates of matching regions between the query and the corresponding database hit sequence. The coordinates are used to plot each matching region as colored lines or trapezoids. Using the straightforward control panels throughout the web site, each plotted matching region can be easily explored in detail by, for example, highlighting the region of interest or examining the raw pair-wise sequence alignment. Tutorials are provided at the website to guide users step-by-step through the functional features of BOV. Conclusion BOV provides a user-friendly web interface to visualize the standard BLAST output for investigating wide-ranging genomic problems, including single query and batch query datasets. In particular, this software is valuable to users interested in identifying regions of co-linearity, duplication, translocation, and inversion among sequences. A web server hosting BOV is accessible via http://bioportal.cgb.indiana.edu/cgi-bin/BOV/index.cgi and the software is freely available for local installations. Blast Program (dpeaa)DE-He213 Matching Region (dpeaa)DE-He213 Query Region (dpeaa)DE-He213 Local Installation (dpeaa)DE-He213 Blast Output (dpeaa)DE-He213 Revanna, Kashi Vishwanath aut Hemmerich, Chris aut Schaack, Sarah aut Dong, Qunfeng aut Enthalten in BMC genomics London : BioMed Central, 2000 9(2008), 1 vom: 15. Sept. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:9 year:2008 number:1 day:15 month:09 https://dx.doi.org/10.1186/1471-2164-9-414 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 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_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 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_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2008 1 15 09
allfields_unstemmed	10.1186/1471-2164-9-414 doi (DE-627)SPR027038041 (SPR)1471-2164-9-414-e DE-627 ger DE-627 rakwb eng Gollapudi, Rajesh verfasserin aut BOV – a web-based BLAST output visualization tool 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Gollapudi et al; licensee BioMed Central Ltd. 2008. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background The BLAST program is one of the most widely used sequence similarity search tools for genomic research, even by those biologists lacking extensive bioinformatics training. As the availability of sequence data increases, more researchers are downloading the BLAST program for local installation and performing larger and more complex tasks, including batch queries. In order to manage and interpret the results of batch queries, a host of software packages have been developed to assist with data management and post-processing. Among these programs, there is almost a complete lack of visualization tools to provide graphic representation of complex BLAST pair-wise alignments. We have developed a web-based program, B LAST O utput V isualization Tool (BOV), that allows users to interactively visualize the matching regions of query and database hit sequences, thereby allowing the user to quickly and easily dissect complex matching patterns. Results Users can upload the standard BLAST output in pair-wise alignment format as input to the web server (including batch queries generated installing and running the stand-alone BLAST program on a local server). The program extracts the alignment coordinates of matching regions between the query and the corresponding database hit sequence. The coordinates are used to plot each matching region as colored lines or trapezoids. Using the straightforward control panels throughout the web site, each plotted matching region can be easily explored in detail by, for example, highlighting the region of interest or examining the raw pair-wise sequence alignment. Tutorials are provided at the website to guide users step-by-step through the functional features of BOV. Conclusion BOV provides a user-friendly web interface to visualize the standard BLAST output for investigating wide-ranging genomic problems, including single query and batch query datasets. In particular, this software is valuable to users interested in identifying regions of co-linearity, duplication, translocation, and inversion among sequences. A web server hosting BOV is accessible via http://bioportal.cgb.indiana.edu/cgi-bin/BOV/index.cgi and the software is freely available for local installations. Blast Program (dpeaa)DE-He213 Matching Region (dpeaa)DE-He213 Query Region (dpeaa)DE-He213 Local Installation (dpeaa)DE-He213 Blast Output (dpeaa)DE-He213 Revanna, Kashi Vishwanath aut Hemmerich, Chris aut Schaack, Sarah aut Dong, Qunfeng aut Enthalten in BMC genomics London : BioMed Central, 2000 9(2008), 1 vom: 15. Sept. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:9 year:2008 number:1 day:15 month:09 https://dx.doi.org/10.1186/1471-2164-9-414 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 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_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 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_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2008 1 15 09
allfieldsGer	10.1186/1471-2164-9-414 doi (DE-627)SPR027038041 (SPR)1471-2164-9-414-e DE-627 ger DE-627 rakwb eng Gollapudi, Rajesh verfasserin aut BOV – a web-based BLAST output visualization tool 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Gollapudi et al; licensee BioMed Central Ltd. 2008. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background The BLAST program is one of the most widely used sequence similarity search tools for genomic research, even by those biologists lacking extensive bioinformatics training. As the availability of sequence data increases, more researchers are downloading the BLAST program for local installation and performing larger and more complex tasks, including batch queries. In order to manage and interpret the results of batch queries, a host of software packages have been developed to assist with data management and post-processing. Among these programs, there is almost a complete lack of visualization tools to provide graphic representation of complex BLAST pair-wise alignments. We have developed a web-based program, B LAST O utput V isualization Tool (BOV), that allows users to interactively visualize the matching regions of query and database hit sequences, thereby allowing the user to quickly and easily dissect complex matching patterns. Results Users can upload the standard BLAST output in pair-wise alignment format as input to the web server (including batch queries generated installing and running the stand-alone BLAST program on a local server). The program extracts the alignment coordinates of matching regions between the query and the corresponding database hit sequence. The coordinates are used to plot each matching region as colored lines or trapezoids. Using the straightforward control panels throughout the web site, each plotted matching region can be easily explored in detail by, for example, highlighting the region of interest or examining the raw pair-wise sequence alignment. Tutorials are provided at the website to guide users step-by-step through the functional features of BOV. Conclusion BOV provides a user-friendly web interface to visualize the standard BLAST output for investigating wide-ranging genomic problems, including single query and batch query datasets. In particular, this software is valuable to users interested in identifying regions of co-linearity, duplication, translocation, and inversion among sequences. A web server hosting BOV is accessible via http://bioportal.cgb.indiana.edu/cgi-bin/BOV/index.cgi and the software is freely available for local installations. Blast Program (dpeaa)DE-He213 Matching Region (dpeaa)DE-He213 Query Region (dpeaa)DE-He213 Local Installation (dpeaa)DE-He213 Blast Output (dpeaa)DE-He213 Revanna, Kashi Vishwanath aut Hemmerich, Chris aut Schaack, Sarah aut Dong, Qunfeng aut Enthalten in BMC genomics London : BioMed Central, 2000 9(2008), 1 vom: 15. Sept. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:9 year:2008 number:1 day:15 month:09 https://dx.doi.org/10.1186/1471-2164-9-414 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 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_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 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_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2008 1 15 09
allfieldsSound	10.1186/1471-2164-9-414 doi (DE-627)SPR027038041 (SPR)1471-2164-9-414-e DE-627 ger DE-627 rakwb eng Gollapudi, Rajesh verfasserin aut BOV – a web-based BLAST output visualization tool 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Gollapudi et al; licensee BioMed Central Ltd. 2008. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background The BLAST program is one of the most widely used sequence similarity search tools for genomic research, even by those biologists lacking extensive bioinformatics training. As the availability of sequence data increases, more researchers are downloading the BLAST program for local installation and performing larger and more complex tasks, including batch queries. In order to manage and interpret the results of batch queries, a host of software packages have been developed to assist with data management and post-processing. Among these programs, there is almost a complete lack of visualization tools to provide graphic representation of complex BLAST pair-wise alignments. We have developed a web-based program, B LAST O utput V isualization Tool (BOV), that allows users to interactively visualize the matching regions of query and database hit sequences, thereby allowing the user to quickly and easily dissect complex matching patterns. Results Users can upload the standard BLAST output in pair-wise alignment format as input to the web server (including batch queries generated installing and running the stand-alone BLAST program on a local server). The program extracts the alignment coordinates of matching regions between the query and the corresponding database hit sequence. The coordinates are used to plot each matching region as colored lines or trapezoids. Using the straightforward control panels throughout the web site, each plotted matching region can be easily explored in detail by, for example, highlighting the region of interest or examining the raw pair-wise sequence alignment. Tutorials are provided at the website to guide users step-by-step through the functional features of BOV. Conclusion BOV provides a user-friendly web interface to visualize the standard BLAST output for investigating wide-ranging genomic problems, including single query and batch query datasets. In particular, this software is valuable to users interested in identifying regions of co-linearity, duplication, translocation, and inversion among sequences. A web server hosting BOV is accessible via http://bioportal.cgb.indiana.edu/cgi-bin/BOV/index.cgi and the software is freely available for local installations. Blast Program (dpeaa)DE-He213 Matching Region (dpeaa)DE-He213 Query Region (dpeaa)DE-He213 Local Installation (dpeaa)DE-He213 Blast Output (dpeaa)DE-He213 Revanna, Kashi Vishwanath aut Hemmerich, Chris aut Schaack, Sarah aut Dong, Qunfeng aut Enthalten in BMC genomics London : BioMed Central, 2000 9(2008), 1 vom: 15. Sept. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:9 year:2008 number:1 day:15 month:09 https://dx.doi.org/10.1186/1471-2164-9-414 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 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_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 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_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2008 1 15 09
language	English
source	Enthalten in BMC genomics 9(2008), 1 vom: 15. Sept. volume:9 year:2008 number:1 day:15 month:09
sourceStr	Enthalten in BMC genomics 9(2008), 1 vom: 15. Sept. volume:9 year:2008 number:1 day:15 month:09
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Blast Program Matching Region Query Region Local Installation Blast Output
isfreeaccess_bool	false
container_title	BMC genomics
authorswithroles_txt_mv	Gollapudi, Rajesh @@aut@@ Revanna, Kashi Vishwanath @@aut@@ Hemmerich, Chris @@aut@@ Schaack, Sarah @@aut@@ Dong, Qunfeng @@aut@@
publishDateDaySort_date	2008-09-15T00:00:00Z
hierarchy_top_id	326644954
id	SPR027038041
language_de	englisch
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author	Gollapudi, Rajesh
spellingShingle	Gollapudi, Rajesh misc Blast Program misc Matching Region misc Query Region misc Local Installation misc Blast Output BOV – a web-based BLAST output visualization tool
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topic_title	BOV – a web-based BLAST output visualization tool Blast Program (dpeaa)DE-He213 Matching Region (dpeaa)DE-He213 Query Region (dpeaa)DE-He213 Local Installation (dpeaa)DE-He213 Blast Output (dpeaa)DE-He213
topic	misc Blast Program misc Matching Region misc Query Region misc Local Installation misc Blast Output
topic_unstemmed	misc Blast Program misc Matching Region misc Query Region misc Local Installation misc Blast Output
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title	BOV – a web-based BLAST output visualization tool
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title_full	BOV – a web-based BLAST output visualization tool
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doi_str_mv	10.1186/1471-2164-9-414
title_sort	bov – a web-based blast output visualization tool
title_auth	BOV – a web-based BLAST output visualization tool
abstract	Background The BLAST program is one of the most widely used sequence similarity search tools for genomic research, even by those biologists lacking extensive bioinformatics training. As the availability of sequence data increases, more researchers are downloading the BLAST program for local installation and performing larger and more complex tasks, including batch queries. In order to manage and interpret the results of batch queries, a host of software packages have been developed to assist with data management and post-processing. Among these programs, there is almost a complete lack of visualization tools to provide graphic representation of complex BLAST pair-wise alignments. We have developed a web-based program, B LAST O utput V isualization Tool (BOV), that allows users to interactively visualize the matching regions of query and database hit sequences, thereby allowing the user to quickly and easily dissect complex matching patterns. Results Users can upload the standard BLAST output in pair-wise alignment format as input to the web server (including batch queries generated installing and running the stand-alone BLAST program on a local server). The program extracts the alignment coordinates of matching regions between the query and the corresponding database hit sequence. The coordinates are used to plot each matching region as colored lines or trapezoids. Using the straightforward control panels throughout the web site, each plotted matching region can be easily explored in detail by, for example, highlighting the region of interest or examining the raw pair-wise sequence alignment. Tutorials are provided at the website to guide users step-by-step through the functional features of BOV. Conclusion BOV provides a user-friendly web interface to visualize the standard BLAST output for investigating wide-ranging genomic problems, including single query and batch query datasets. In particular, this software is valuable to users interested in identifying regions of co-linearity, duplication, translocation, and inversion among sequences. A web server hosting BOV is accessible via http://bioportal.cgb.indiana.edu/cgi-bin/BOV/index.cgi and the software is freely available for local installations. © Gollapudi et al; licensee BioMed Central Ltd. 2008. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (
abstractGer	Background The BLAST program is one of the most widely used sequence similarity search tools for genomic research, even by those biologists lacking extensive bioinformatics training. As the availability of sequence data increases, more researchers are downloading the BLAST program for local installation and performing larger and more complex tasks, including batch queries. In order to manage and interpret the results of batch queries, a host of software packages have been developed to assist with data management and post-processing. Among these programs, there is almost a complete lack of visualization tools to provide graphic representation of complex BLAST pair-wise alignments. We have developed a web-based program, B LAST O utput V isualization Tool (BOV), that allows users to interactively visualize the matching regions of query and database hit sequences, thereby allowing the user to quickly and easily dissect complex matching patterns. Results Users can upload the standard BLAST output in pair-wise alignment format as input to the web server (including batch queries generated installing and running the stand-alone BLAST program on a local server). The program extracts the alignment coordinates of matching regions between the query and the corresponding database hit sequence. The coordinates are used to plot each matching region as colored lines or trapezoids. Using the straightforward control panels throughout the web site, each plotted matching region can be easily explored in detail by, for example, highlighting the region of interest or examining the raw pair-wise sequence alignment. Tutorials are provided at the website to guide users step-by-step through the functional features of BOV. Conclusion BOV provides a user-friendly web interface to visualize the standard BLAST output for investigating wide-ranging genomic problems, including single query and batch query datasets. In particular, this software is valuable to users interested in identifying regions of co-linearity, duplication, translocation, and inversion among sequences. A web server hosting BOV is accessible via http://bioportal.cgb.indiana.edu/cgi-bin/BOV/index.cgi and the software is freely available for local installations. © Gollapudi et al; licensee BioMed Central Ltd. 2008. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (
abstract_unstemmed	Background The BLAST program is one of the most widely used sequence similarity search tools for genomic research, even by those biologists lacking extensive bioinformatics training. As the availability of sequence data increases, more researchers are downloading the BLAST program for local installation and performing larger and more complex tasks, including batch queries. In order to manage and interpret the results of batch queries, a host of software packages have been developed to assist with data management and post-processing. Among these programs, there is almost a complete lack of visualization tools to provide graphic representation of complex BLAST pair-wise alignments. We have developed a web-based program, B LAST O utput V isualization Tool (BOV), that allows users to interactively visualize the matching regions of query and database hit sequences, thereby allowing the user to quickly and easily dissect complex matching patterns. Results Users can upload the standard BLAST output in pair-wise alignment format as input to the web server (including batch queries generated installing and running the stand-alone BLAST program on a local server). The program extracts the alignment coordinates of matching regions between the query and the corresponding database hit sequence. The coordinates are used to plot each matching region as colored lines or trapezoids. Using the straightforward control panels throughout the web site, each plotted matching region can be easily explored in detail by, for example, highlighting the region of interest or examining the raw pair-wise sequence alignment. Tutorials are provided at the website to guide users step-by-step through the functional features of BOV. Conclusion BOV provides a user-friendly web interface to visualize the standard BLAST output for investigating wide-ranging genomic problems, including single query and batch query datasets. In particular, this software is valuable to users interested in identifying regions of co-linearity, duplication, translocation, and inversion among sequences. A web server hosting BOV is accessible via http://bioportal.cgb.indiana.edu/cgi-bin/BOV/index.cgi and the software is freely available for local installations. © Gollapudi et al; licensee BioMed Central Ltd. 2008. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (
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title_short	BOV – a web-based BLAST output visualization tool
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