Gene finding in the chicken genome
<p>Abstract</p> <p>Background</p> <p>Despite the continuous production of genome sequence for a number of organisms, reliable, comprehensive, and cost effective gene prediction remains problematic. This is particularly true for genomes for which there is not a large col...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2005-05-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/6/131 |
| _version_ | 1811252347460911104 |
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| author | Antonarakis Stylianos E Rogers Jane Wyss Carine Shteynberg David D Huckle Elizabeth J Parra Genis Flicek Paul Camara Francisco Bye Jacqueline M Castelo Robert Reymond Alexandre Eyras Eduardo Birney Ewan Guigo Roderic Brent Michael R |
| author_facet | Antonarakis Stylianos E Rogers Jane Wyss Carine Shteynberg David D Huckle Elizabeth J Parra Genis Flicek Paul Camara Francisco Bye Jacqueline M Castelo Robert Reymond Alexandre Eyras Eduardo Birney Ewan Guigo Roderic Brent Michael R |
| author_sort | Antonarakis Stylianos E |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Despite the continuous production of genome sequence for a number of organisms, reliable, comprehensive, and cost effective gene prediction remains problematic. This is particularly true for genomes for which there is not a large collection of known gene sequences, such as the recently published chicken genome. We used the chicken sequence to test comparative and homology-based gene-finding methods followed by experimental validation as an effective genome annotation method.</p> <p>Results</p> <p>We performed experimental evaluation by RT-PCR of three different computational gene finders, Ensembl, SGP2 and TWINSCAN, applied to the chicken genome. A Venn diagram was computed and each component of it was evaluated. The results showed that <it>de novo </it>comparative methods can identify up to about 700 chicken genes with no previous evidence of expression, and can correctly extend about 40% of homology-based predictions at the 5' end.</p> <p>Conclusions</p> <p><it>De novo </it>comparative gene prediction followed by experimental verification is effective at enhancing the annotation of the newly sequenced genomes provided by standard homology-based methods.</p> |
| first_indexed | 2024-04-12T16:33:23Z |
| format | Article |
| id | doaj.art-f7ea396c67c5441eb41504d142899659 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-12T16:33:23Z |
| publishDate | 2005-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-f7ea396c67c5441eb41504d1428996592022-12-22T03:25:04ZengBMCBMC Bioinformatics1471-21052005-05-016113110.1186/1471-2105-6-131Gene finding in the chicken genomeAntonarakis Stylianos ERogers JaneWyss CarineShteynberg David DHuckle Elizabeth JParra GenisFlicek PaulCamara FranciscoBye Jacqueline MCastelo RobertReymond AlexandreEyras EduardoBirney EwanGuigo RodericBrent Michael R<p>Abstract</p> <p>Background</p> <p>Despite the continuous production of genome sequence for a number of organisms, reliable, comprehensive, and cost effective gene prediction remains problematic. This is particularly true for genomes for which there is not a large collection of known gene sequences, such as the recently published chicken genome. We used the chicken sequence to test comparative and homology-based gene-finding methods followed by experimental validation as an effective genome annotation method.</p> <p>Results</p> <p>We performed experimental evaluation by RT-PCR of three different computational gene finders, Ensembl, SGP2 and TWINSCAN, applied to the chicken genome. A Venn diagram was computed and each component of it was evaluated. The results showed that <it>de novo </it>comparative methods can identify up to about 700 chicken genes with no previous evidence of expression, and can correctly extend about 40% of homology-based predictions at the 5' end.</p> <p>Conclusions</p> <p><it>De novo </it>comparative gene prediction followed by experimental verification is effective at enhancing the annotation of the newly sequenced genomes provided by standard homology-based methods.</p>http://www.biomedcentral.com/1471-2105/6/131 |
| spellingShingle | Antonarakis Stylianos E Rogers Jane Wyss Carine Shteynberg David D Huckle Elizabeth J Parra Genis Flicek Paul Camara Francisco Bye Jacqueline M Castelo Robert Reymond Alexandre Eyras Eduardo Birney Ewan Guigo Roderic Brent Michael R Gene finding in the chicken genome BMC Bioinformatics |
| title | Gene finding in the chicken genome |
| title_full | Gene finding in the chicken genome |
| title_fullStr | Gene finding in the chicken genome |
| title_full_unstemmed | Gene finding in the chicken genome |
| title_short | Gene finding in the chicken genome |
| title_sort | gene finding in the chicken genome |
| url | http://www.biomedcentral.com/1471-2105/6/131 |
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