The Ensembl gene annotation system
The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological s...
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| Published in | Database : the journal of biological databases and curation Vol. 2016; p. baw093 |
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| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford University Press
2016
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| Subjects | |
| Online Access | Get full text |
| ISSN | 1758-0463 1758-0463 |
| DOI | 10.1093/database/baw093 |
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| Abstract | The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail.Database URL: http://www.ensembl.org/index.html. |
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| AbstractList | The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail.Database URL: http://www.ensembl.org/index.html. The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail. Database URL: http://www.ensembl.org/index.html The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail.Database URL: http://www.ensembl.org/index.html.The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail.Database URL: http://www.ensembl.org/index.html. The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail. |
| Author | Curwen, Valery Zadissa, Amonida Tang, Y. Amy Billis, Konstantinos White, Simon Searle, Stephen M. J. Barrell, Daniel Kokocinski, Felix Aken, Bronwen L. Ayling, Sarah Vogel, Jan-Hinnerk Fairley, Susan Fernandez Banet, Julio Clarke, Laura Hourlier, Thibaut Howe, Kevin Martin, Fergal J. Flicek, Paul Schuster, Michael Ruffier, Magali Nag, Rishi Kähäri, Andreas García Girón, Carlos Murphy, Daniel N. |
| Author_xml | – sequence: 1 givenname: Bronwen L. surname: Aken fullname: Aken, Bronwen L. – sequence: 2 givenname: Sarah surname: Ayling fullname: Ayling, Sarah – sequence: 3 givenname: Daniel surname: Barrell fullname: Barrell, Daniel – sequence: 4 givenname: Laura surname: Clarke fullname: Clarke, Laura – sequence: 5 givenname: Valery surname: Curwen fullname: Curwen, Valery – sequence: 6 givenname: Susan surname: Fairley fullname: Fairley, Susan – sequence: 7 givenname: Julio surname: Fernandez Banet fullname: Fernandez Banet, Julio – sequence: 8 givenname: Konstantinos surname: Billis fullname: Billis, Konstantinos – sequence: 9 givenname: Carlos surname: García Girón fullname: García Girón, Carlos – sequence: 10 givenname: Thibaut surname: Hourlier fullname: Hourlier, Thibaut – sequence: 11 givenname: Kevin surname: Howe fullname: Howe, Kevin – sequence: 12 givenname: Andreas surname: Kähäri fullname: Kähäri, Andreas – sequence: 13 givenname: Felix surname: Kokocinski fullname: Kokocinski, Felix – sequence: 14 givenname: Fergal J. surname: Martin fullname: Martin, Fergal J. – sequence: 15 givenname: Daniel N. surname: Murphy fullname: Murphy, Daniel N. – sequence: 16 givenname: Rishi surname: Nag fullname: Nag, Rishi – sequence: 17 givenname: Magali surname: Ruffier fullname: Ruffier, Magali – sequence: 18 givenname: Michael surname: Schuster fullname: Schuster, Michael – sequence: 19 givenname: Y. Amy surname: Tang fullname: Tang, Y. Amy – sequence: 20 givenname: Jan-Hinnerk surname: Vogel fullname: Vogel, Jan-Hinnerk – sequence: 21 givenname: Simon surname: White fullname: White, Simon – sequence: 22 givenname: Amonida surname: Zadissa fullname: Zadissa, Amonida – sequence: 23 givenname: Paul surname: Flicek fullname: Flicek, Paul – sequence: 24 givenname: Stephen M. J. surname: Searle fullname: Searle, Stephen M. J. |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/27337980$$D View this record in MEDLINE/PubMed https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-304531$$DView record from Swedish Publication Index |
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| Snippet | The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it... |
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| Title | The Ensembl gene annotation system |
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