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Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms
BACKGROUND: Complete genome annotation is a necessary tool as Anopheles gambiae researchers probe the biology of this potent malaria vector. RESULTS: We reannotate the A. gambiae genome by synthesizing comparative and ab initio sets of predicted coding sequences (CDSs) into a single set using an exo...
Autores principales: | , , , , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2006
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1557760/ https://www.ncbi.nlm.nih.gov/pubmed/16569258 http://dx.doi.org/10.1186/gb-2006-7-3-r24 |
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author | Li, Jun Riehle, Michelle M Zhang, Yan Xu, Jiannong Oduol, Frederick Gomez, Shawn M Eiglmeier, Karin Ueberheide, Beatrix M Shabanowitz, Jeffrey Hunt, Donald F Ribeiro, José MC Vernick, Kenneth D |
author_facet | Li, Jun Riehle, Michelle M Zhang, Yan Xu, Jiannong Oduol, Frederick Gomez, Shawn M Eiglmeier, Karin Ueberheide, Beatrix M Shabanowitz, Jeffrey Hunt, Donald F Ribeiro, José MC Vernick, Kenneth D |
author_sort | Li, Jun |
collection | PubMed |
description | BACKGROUND: Complete genome annotation is a necessary tool as Anopheles gambiae researchers probe the biology of this potent malaria vector. RESULTS: We reannotate the A. gambiae genome by synthesizing comparative and ab initio sets of predicted coding sequences (CDSs) into a single set using an exon-gene-union algorithm followed by an open-reading-frame-selection algorithm. The reannotation predicts 20,970 CDSs supported by at least two lines of evidence, and it lowers the proportion of CDSs lacking start and/or stop codons to only approximately 4%. The reannotated CDS set includes a set of 4,681 novel CDSs not represented in the Ensembl annotation but with EST support, and another set of 4,031 Ensembl-supported genes that undergo major structural and, therefore, probably functional changes in the reannotated set. The quality and accuracy of the reannotation was assessed by comparison with end sequences from 20,249 full-length cDNA clones, and evaluation of mass spectrometry peptide hit rates from an A. gambiae shotgun proteomic dataset confirms that the reannotated CDSs offer a high quality protein database for proteomics. We provide a functional proteomics annotation, ReAnoXcel, obtained by analysis of the new CDSs through the AnoXcel pipeline, which allows functional comparisons of the CDS sets within the same bioinformatic platform. CDS data are available for download. CONCLUSION: Comprehensive A. gambiae genome reannotation is achieved through a combination of comparative and ab initio gene prediction algorithms. |
format | Text |
id | pubmed-1557760 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2006 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-15577602006-09-01 Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms Li, Jun Riehle, Michelle M Zhang, Yan Xu, Jiannong Oduol, Frederick Gomez, Shawn M Eiglmeier, Karin Ueberheide, Beatrix M Shabanowitz, Jeffrey Hunt, Donald F Ribeiro, José MC Vernick, Kenneth D Genome Biol Research BACKGROUND: Complete genome annotation is a necessary tool as Anopheles gambiae researchers probe the biology of this potent malaria vector. RESULTS: We reannotate the A. gambiae genome by synthesizing comparative and ab initio sets of predicted coding sequences (CDSs) into a single set using an exon-gene-union algorithm followed by an open-reading-frame-selection algorithm. The reannotation predicts 20,970 CDSs supported by at least two lines of evidence, and it lowers the proportion of CDSs lacking start and/or stop codons to only approximately 4%. The reannotated CDS set includes a set of 4,681 novel CDSs not represented in the Ensembl annotation but with EST support, and another set of 4,031 Ensembl-supported genes that undergo major structural and, therefore, probably functional changes in the reannotated set. The quality and accuracy of the reannotation was assessed by comparison with end sequences from 20,249 full-length cDNA clones, and evaluation of mass spectrometry peptide hit rates from an A. gambiae shotgun proteomic dataset confirms that the reannotated CDSs offer a high quality protein database for proteomics. We provide a functional proteomics annotation, ReAnoXcel, obtained by analysis of the new CDSs through the AnoXcel pipeline, which allows functional comparisons of the CDS sets within the same bioinformatic platform. CDS data are available for download. CONCLUSION: Comprehensive A. gambiae genome reannotation is achieved through a combination of comparative and ab initio gene prediction algorithms. BioMed Central 2006 2006-03-27 /pmc/articles/PMC1557760/ /pubmed/16569258 http://dx.doi.org/10.1186/gb-2006-7-3-r24 Text en Copyright © 2006 Li et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Li, Jun Riehle, Michelle M Zhang, Yan Xu, Jiannong Oduol, Frederick Gomez, Shawn M Eiglmeier, Karin Ueberheide, Beatrix M Shabanowitz, Jeffrey Hunt, Donald F Ribeiro, José MC Vernick, Kenneth D Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms |
title | Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms |
title_full | Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms |
title_fullStr | Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms |
title_full_unstemmed | Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms |
title_short | Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms |
title_sort | anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1557760/ https://www.ncbi.nlm.nih.gov/pubmed/16569258 http://dx.doi.org/10.1186/gb-2006-7-3-r24 |
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