Syntenator: Multiple gene order alignments with a gene-specific scoring function
<p>Abstract</p> <p>Background</p> <p>Identification of homologous regions or conserved syntenies across genomes is one crucial step in comparative genomics. This task is usually performed by genome alignment softwares like WABA or blastz. In case of conserved syntenies,...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2008-11-01
|
| Series: | Algorithms for Molecular Biology |
| Online Access: | http://www.almob.org/content/3/1/14 |
| _version_ | 1818496273374773248 |
|---|---|
| author | Dieterich Christoph Rödelsperger Christian |
| author_facet | Dieterich Christoph Rödelsperger Christian |
| author_sort | Dieterich Christoph |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Identification of homologous regions or conserved syntenies across genomes is one crucial step in comparative genomics. This task is usually performed by genome alignment softwares like WABA or blastz. In case of conserved syntenies, such regions are defined as conserved gene orders. On the gene order level, homologous regions can even be found between distantly related genomes, which do not align on the nucleotide sequence level.</p> <p>Results</p> <p>We present a novel approach to identify regions of conserved synteny across multiple genomes. Syntenator represents genomes and alignments thereof as partial order graphs (POGs). These POGs are aligned by a dynamic programming approach employing a gene-specific scoring function. The scoring function reflects the level of protein sequence similarity for each possible gene pair. Our method consistently defines larger homologous regions in pairwise gene order alignments than nucleotide-level comparisons. Our method is superior to methods that work on predefined homology gene sets (as implemented in Blockfinder). Syntenator successfully reproduces 80% of the EnsEMBL man-mouse conserved syntenic blocks. The full potential of our method becomes visible by comparing remotely related genomes and multiple genomes. Gene order alignments potentially resolve up to 75% of the EnsEMBL 1:many orthology relations and 27% of the many:many orthology relations.</p> <p>Conclusion</p> <p>We propose Syntenator as a software solution to reliably infer conserved syntenies among distantly related genomes. The software is available from <url>http://www2.tuebingen.mpg.de/abt4/plone</url>.</p> |
| first_indexed | 2024-12-10T18:31:18Z |
| format | Article |
| id | doaj.art-4b02d8d685914c358ae143d8b423b431 |
| institution | Directory Open Access Journal |
| issn | 1748-7188 |
| language | English |
| last_indexed | 2024-12-10T18:31:18Z |
| publishDate | 2008-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Algorithms for Molecular Biology |
| spelling | doaj.art-4b02d8d685914c358ae143d8b423b4312022-12-22T01:37:56ZengBMCAlgorithms for Molecular Biology1748-71882008-11-01311410.1186/1748-7188-3-14Syntenator: Multiple gene order alignments with a gene-specific scoring functionDieterich ChristophRödelsperger Christian<p>Abstract</p> <p>Background</p> <p>Identification of homologous regions or conserved syntenies across genomes is one crucial step in comparative genomics. This task is usually performed by genome alignment softwares like WABA or blastz. In case of conserved syntenies, such regions are defined as conserved gene orders. On the gene order level, homologous regions can even be found between distantly related genomes, which do not align on the nucleotide sequence level.</p> <p>Results</p> <p>We present a novel approach to identify regions of conserved synteny across multiple genomes. Syntenator represents genomes and alignments thereof as partial order graphs (POGs). These POGs are aligned by a dynamic programming approach employing a gene-specific scoring function. The scoring function reflects the level of protein sequence similarity for each possible gene pair. Our method consistently defines larger homologous regions in pairwise gene order alignments than nucleotide-level comparisons. Our method is superior to methods that work on predefined homology gene sets (as implemented in Blockfinder). Syntenator successfully reproduces 80% of the EnsEMBL man-mouse conserved syntenic blocks. The full potential of our method becomes visible by comparing remotely related genomes and multiple genomes. Gene order alignments potentially resolve up to 75% of the EnsEMBL 1:many orthology relations and 27% of the many:many orthology relations.</p> <p>Conclusion</p> <p>We propose Syntenator as a software solution to reliably infer conserved syntenies among distantly related genomes. The software is available from <url>http://www2.tuebingen.mpg.de/abt4/plone</url>.</p>http://www.almob.org/content/3/1/14 |
| spellingShingle | Dieterich Christoph Rödelsperger Christian Syntenator: Multiple gene order alignments with a gene-specific scoring function Algorithms for Molecular Biology |
| title | Syntenator: Multiple gene order alignments with a gene-specific scoring function |
| title_full | Syntenator: Multiple gene order alignments with a gene-specific scoring function |
| title_fullStr | Syntenator: Multiple gene order alignments with a gene-specific scoring function |
| title_full_unstemmed | Syntenator: Multiple gene order alignments with a gene-specific scoring function |
| title_short | Syntenator: Multiple gene order alignments with a gene-specific scoring function |
| title_sort | syntenator multiple gene order alignments with a gene specific scoring function |
| url | http://www.almob.org/content/3/1/14 |
| work_keys_str_mv | AT dieterichchristoph syntenatormultiplegeneorderalignmentswithagenespecificscoringfunction AT rodelspergerchristian syntenatormultiplegeneorderalignmentswithagenespecificscoringfunction |