Enrichment of homologs in insignificant BLAST hits by co-complex network alignment
<p>Abstract</p> <p>Background</p> <p>Homology is a crucial concept in comparative genomics. The algorithm probably most widely used for homology detection in comparative genomics, is BLAST. Usually a stringent score cutoff is applied to distinguish putative homologs fro...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2010-02-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/11/86 |
| _version_ | 1811313973462564864 |
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| author | Boekhorst Jos Botelho Sandra MC Fokkens Like Snel Berend |
| author_facet | Boekhorst Jos Botelho Sandra MC Fokkens Like Snel Berend |
| author_sort | Boekhorst Jos |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Homology is a crucial concept in comparative genomics. The algorithm probably most widely used for homology detection in comparative genomics, is BLAST. Usually a stringent score cutoff is applied to distinguish putative homologs from possible false positive hits. As a consequence, some BLAST hits are discarded that are in fact homologous.</p> <p>Results</p> <p>Analogous to the use of the genomics context in genome alignments, we test whether conserved functional context can be used to select candidate homologs from insignificant BLAST hits. We make a co-complex network alignment between complex subunits in yeast and human and find that proteins with an insignificant BLAST hit that are part of homologous complexes, are likely to be homologous themselves. Further analysis of the distant homologs we recovered using the co-complex network alignment, shows that a large majority of these distant homologs are in fact ancient paralogs.</p> <p>Conclusions</p> <p>Our results show that, even though evolution takes place at the sequence and genome level, co-complex networks can be used as circumstantial evidence to improve confidence in the homology of distantly related sequences.</p> |
| first_indexed | 2024-04-13T11:03:47Z |
| format | Article |
| id | doaj.art-de8797660b5d48f7828b4113fadf9d39 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-13T11:03:47Z |
| publishDate | 2010-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-de8797660b5d48f7828b4113fadf9d392022-12-22T02:49:20ZengBMCBMC Bioinformatics1471-21052010-02-011118610.1186/1471-2105-11-86Enrichment of homologs in insignificant BLAST hits by co-complex network alignmentBoekhorst JosBotelho Sandra MCFokkens LikeSnel Berend<p>Abstract</p> <p>Background</p> <p>Homology is a crucial concept in comparative genomics. The algorithm probably most widely used for homology detection in comparative genomics, is BLAST. Usually a stringent score cutoff is applied to distinguish putative homologs from possible false positive hits. As a consequence, some BLAST hits are discarded that are in fact homologous.</p> <p>Results</p> <p>Analogous to the use of the genomics context in genome alignments, we test whether conserved functional context can be used to select candidate homologs from insignificant BLAST hits. We make a co-complex network alignment between complex subunits in yeast and human and find that proteins with an insignificant BLAST hit that are part of homologous complexes, are likely to be homologous themselves. Further analysis of the distant homologs we recovered using the co-complex network alignment, shows that a large majority of these distant homologs are in fact ancient paralogs.</p> <p>Conclusions</p> <p>Our results show that, even though evolution takes place at the sequence and genome level, co-complex networks can be used as circumstantial evidence to improve confidence in the homology of distantly related sequences.</p>http://www.biomedcentral.com/1471-2105/11/86 |
| spellingShingle | Boekhorst Jos Botelho Sandra MC Fokkens Like Snel Berend Enrichment of homologs in insignificant BLAST hits by co-complex network alignment BMC Bioinformatics |
| title | Enrichment of homologs in insignificant BLAST hits by co-complex network alignment |
| title_full | Enrichment of homologs in insignificant BLAST hits by co-complex network alignment |
| title_fullStr | Enrichment of homologs in insignificant BLAST hits by co-complex network alignment |
| title_full_unstemmed | Enrichment of homologs in insignificant BLAST hits by co-complex network alignment |
| title_short | Enrichment of homologs in insignificant BLAST hits by co-complex network alignment |
| title_sort | enrichment of homologs in insignificant blast hits by co complex network alignment |
| url | http://www.biomedcentral.com/1471-2105/11/86 |
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