Gene finding in the chicken genome
| العنوان: | Gene finding in the chicken genome |
|---|---|
| المؤلفون: | Eduardo, Eyras, Alexandre, Reymond, Robert, Castelo, Jacqueline M, Bye, Francisco, Camara, Paul, Flicek, Elizabeth J, Huckle, Genis, Parra, David D, Shteynberg, Carine, Wyss, Jane, Rogers, Stylianos E, Antonarakis, Ewan, Birney, Roderic, Guigo, Michael R, Brent |
| المساهمون: | Universitat Pompeu Fabra |
| المصدر: | BMC Bioinformatics, Vol. 6 (2005) P. 131 BMC Bioinformatics, Vol 6, Iss 1, p 131 (2005) BMC Bioinformatics, vol. 6, pp. 131 Recercat. Dipósit de la Recerca de Catalunya instname BMC Bioinformatics |
| بيانات النشر: | BioMed Central, 2005. |
| سنة النشر: | 2005 |
| مصطلحات موضوعية: | DNA, Complementary, DNA, Complementary/metabolism, Genètica -- Tècnica, lcsh:Computer applications to medicine. Medical informatics, Seqüència d'aminoàcids, Databases, Genetic, Animals, ddc:576.5, Tissue Distribution, Chickens, Chromosome Mapping, Computational Biology/methods, DNA Primers, Data Interpretation, Statistical, Exons, Expressed Sequence Tags, Gene Expression Profiling, Genome, Introns, Models, Statistical, Reverse Transcriptase Polymerase Chain Reaction, Sequence Alignment, Sequence Analysis, DNA, Software, lcsh:QH301-705.5, DNA sequence analysis, Computational Biology/ methods, Biologia computacional -- Mètodes, Genòmica -- Bases de dades, Computational Biology, lcsh:Biology (General), lcsh:R858-859.7, cDNA, Genòmica -- Models estadístics, Research Article |
| الوصف: | Background: Despite the continuous production of genome sequence for a number of organisms,/nreliable, comprehensive, and cost effective gene prediction remains problematic. This is particularly/ntrue for genomes for which there is not a large collection of known gene sequences, such as the/nrecently published chicken genome. We used the chicken sequence to test comparative and/nhomology-based gene-finding methods followed by experimental validation as an effective genome/nannotation method./nResults: We performed experimental evaluation by RT-PCR of three different computational gene/nfinders, Ensembl, SGP2 and TWINSCAN, applied to the chicken genome. A Venn diagram was/ncomputed and each component of it was evaluated. The results showed that de novo comparative/nmethods can identify up to about 700 chicken genes with no previous evidence of expression, and/ncan correctly extend about 40% of homology-based predictions at the 5' end./nConclusions: De novo comparative gene prediction followed by experimental verification is/neffective at enhancing the annotation of the newly sequenced genomes provided by standard/nhomology-based methods. This work was supported by grants from the Jérôme Lejeune,/nChildcare and Désirée and Niels Yde Foundations, the European Union, the/nSwiss National Science Foundation and the NCCR Frontiers in Genetics. E/nEyras is funded by the Institució Catalana de Recerca I Estudis Avançats/n(ICREA). R Guigo's lab acknowledges support from grants from the/nNational Plan for R&D (Spain), QLK3-CT-2002-02062 from the European/nCommunity and HG003150-01 from the National Institutes of Health./nResearch on gene prediction by vertebrate genome comparison in the/nBrent lab is supported by grant R01 HG02278 from the National Institutes/nof Health. This work was also supported by EMBL and the Wellcome Trust. |
| وصف الملف: | application/pdf |
| اللغة: | English |
| تدمد: | 1471-2105 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=pmid_dedup__::747400740de93463795a82b12411e118 http://hdl.handle.net/10230/13154 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.pmid.dedup....747400740de93463795a82b12411e118 |
| قاعدة البيانات: | OpenAIRE |
Find this article in full text from Springer Verlag. | تدمد: | 14712105 |
|---|