CGUG: <it>in silico </it>proteome and genome parsing tool for the determination of "core" and unique genes in the analysis of genomes up to <it>ca</it>. 1.9 Mb
<p>Abstract</p> <p>Background</p> <p>Viruses and small-genome bacteria (~2 megabases and smaller) comprise a considerable population in the biosphere and are of interest to many researchers. These genomes are now sequenced at an unprecedented rate and require complement...
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| Format: | Article |
| Language: | English |
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BMC
2009-08-01
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| Series: | BMC Research Notes |
| Online Access: | http://www.biomedcentral.com/1756-0500-2-168 |
| _version_ | 1811287224514248704 |
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| author | Mahadevan Padmanabhan King John F Seto Donald |
| author_facet | Mahadevan Padmanabhan King John F Seto Donald |
| author_sort | Mahadevan Padmanabhan |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Viruses and small-genome bacteria (~2 megabases and smaller) comprise a considerable population in the biosphere and are of interest to many researchers. These genomes are now sequenced at an unprecedented rate and require complementary computational tools to analyze. "CoreGenesUniqueGenes" (CGUG) is an <it>in silico </it>genome data mining tool that determines a "core" set of genes from two to five organisms with genomes in this size range. Core and unique genes may reflect similar niches and needs, and may be used in classifying organisms.</p> <p>Findings</p> <p>CGUG is available at <url>http://binf.gmu.edu/geneorder.html</url> as a web-based on-the-fly tool that performs iterative BLASTP analyses using a reference genome and up to four query genomes to provide a table of genes common to these genomes. The result is an <it>in silico </it>display of genomes and their proteomes, allowing for further analysis. CGUG can be used for "genome annotation by homology", as demonstrated with <it>Chlamydophila </it>and <it>Francisella </it>genomes.</p> <p>Conclusion</p> <p>CGUG is used to reanalyze the ICTV-based classifications of bacteriophages, to reconfirm long-standing relationships and to explore new classifications. These genomes have been problematic in the past, due largely to horizontal gene transfers. CGUG is validated as a tool for reannotating small genome bacteria using more up-to-date annotations by similarity or homology. These serve as an entry point for wet-bench experiments to confirm the functions of these "hypothetical" and "unknown" proteins.</p> |
| first_indexed | 2024-04-13T03:14:58Z |
| format | Article |
| id | doaj.art-191302300c56430d9e7f065a9643ba74 |
| institution | Directory Open Access Journal |
| issn | 1756-0500 |
| language | English |
| last_indexed | 2024-04-13T03:14:58Z |
| publishDate | 2009-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Research Notes |
| spelling | doaj.art-191302300c56430d9e7f065a9643ba742022-12-22T03:04:56ZengBMCBMC Research Notes1756-05002009-08-012116810.1186/1756-0500-2-168CGUG: <it>in silico </it>proteome and genome parsing tool for the determination of "core" and unique genes in the analysis of genomes up to <it>ca</it>. 1.9 MbMahadevan PadmanabhanKing John FSeto Donald<p>Abstract</p> <p>Background</p> <p>Viruses and small-genome bacteria (~2 megabases and smaller) comprise a considerable population in the biosphere and are of interest to many researchers. These genomes are now sequenced at an unprecedented rate and require complementary computational tools to analyze. "CoreGenesUniqueGenes" (CGUG) is an <it>in silico </it>genome data mining tool that determines a "core" set of genes from two to five organisms with genomes in this size range. Core and unique genes may reflect similar niches and needs, and may be used in classifying organisms.</p> <p>Findings</p> <p>CGUG is available at <url>http://binf.gmu.edu/geneorder.html</url> as a web-based on-the-fly tool that performs iterative BLASTP analyses using a reference genome and up to four query genomes to provide a table of genes common to these genomes. The result is an <it>in silico </it>display of genomes and their proteomes, allowing for further analysis. CGUG can be used for "genome annotation by homology", as demonstrated with <it>Chlamydophila </it>and <it>Francisella </it>genomes.</p> <p>Conclusion</p> <p>CGUG is used to reanalyze the ICTV-based classifications of bacteriophages, to reconfirm long-standing relationships and to explore new classifications. These genomes have been problematic in the past, due largely to horizontal gene transfers. CGUG is validated as a tool for reannotating small genome bacteria using more up-to-date annotations by similarity or homology. These serve as an entry point for wet-bench experiments to confirm the functions of these "hypothetical" and "unknown" proteins.</p>http://www.biomedcentral.com/1756-0500-2-168 |
| spellingShingle | Mahadevan Padmanabhan King John F Seto Donald CGUG: <it>in silico </it>proteome and genome parsing tool for the determination of "core" and unique genes in the analysis of genomes up to <it>ca</it>. 1.9 Mb BMC Research Notes |
| title | CGUG: <it>in silico </it>proteome and genome parsing tool for the determination of "core" and unique genes in the analysis of genomes up to <it>ca</it>. 1.9 Mb |
| title_full | CGUG: <it>in silico </it>proteome and genome parsing tool for the determination of "core" and unique genes in the analysis of genomes up to <it>ca</it>. 1.9 Mb |
| title_fullStr | CGUG: <it>in silico </it>proteome and genome parsing tool for the determination of "core" and unique genes in the analysis of genomes up to <it>ca</it>. 1.9 Mb |
| title_full_unstemmed | CGUG: <it>in silico </it>proteome and genome parsing tool for the determination of "core" and unique genes in the analysis of genomes up to <it>ca</it>. 1.9 Mb |
| title_short | CGUG: <it>in silico </it>proteome and genome parsing tool for the determination of "core" and unique genes in the analysis of genomes up to <it>ca</it>. 1.9 Mb |
| title_sort | cgug it in silico it proteome and genome parsing tool for the determination of core and unique genes in the analysis of genomes up to it ca it 1 9 mb |
| url | http://www.biomedcentral.com/1756-0500-2-168 |
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