AVATAR: A database for genome-wide alternative splicing event detection using large scale ESTs and mRNAs

In the past years, identification of alternative splicing (AS) variants has been gaining momentum. We developed AVATAR, a database for documenting AS using 5,469,433 human EST sequences and 26,159 human mRNA sequences. AVATAR contains 12000 alternative splicing sites identified by mapping ESTs and m...

Descripción completa

Detalles Bibliográficos
Autores principales: Hsu, Fang Rong, Chang, Hwan-You, Lin, Yaw-Lin, Tsai, Yin-Te, Peng, Hui-Ling, Chen, Ying Tsong, Cheng, Chia Yang, Shih, Min Yao, Liu, Chia-Hung, Chen, Chin-Feng
Formato: Texto
Lenguaje:English
Publicado: Biomedical Informatics Publishing Group 2005
Materias:
Web Database
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891626/
https://www.ncbi.nlm.nih.gov/pubmed/17597845
_version_ 1782133762713190400
author Hsu, Fang Rong
Chang, Hwan-You
Lin, Yaw-Lin
Tsai, Yin-Te
Peng, Hui-Ling
Chen, Ying Tsong
Cheng, Chia Yang
Shih, Min Yao
Liu, Chia-Hung
Chen, Chin-Feng
author_facet Hsu, Fang Rong
Chang, Hwan-You
Lin, Yaw-Lin
Tsai, Yin-Te
Peng, Hui-Ling
Chen, Ying Tsong
Cheng, Chia Yang
Shih, Min Yao
Liu, Chia-Hung
Chen, Chin-Feng
author_sort Hsu, Fang Rong
collection PubMed
description In the past years, identification of alternative splicing (AS) variants has been gaining momentum. We developed AVATAR, a database for documenting AS using 5,469,433 human EST sequences and 26,159 human mRNA sequences. AVATAR contains 12000 alternative splicing sites identified by mapping ESTs and mRNAs with the whole human genome sequence. AVATAR also contains AS information for 6 eukaryotes. We mapped EST alignment information into a graph model where exons and introns are represented with vertices and edges, respectively. AVATAR can be queried using, (1) gene names, (2) number of identified AS events in a gene, (3) minimal number of ESTs supporting a splicing site, etc. as search parameters. The system provides visualized AS information for queried genes. AVAILABILITY: The database is available for free at http://avatar.iecs.fcu.edu.tw/
format Text
id pubmed-1891626
institution National Center for Biotechnology Information
language English
publishDate 2005
publisher Biomedical Informatics Publishing Group
record_format MEDLINE/PubMed
spelling pubmed-18916262007-06-27 AVATAR: A database for genome-wide alternative splicing event detection using large scale ESTs and mRNAs Hsu, Fang Rong Chang, Hwan-You Lin, Yaw-Lin Tsai, Yin-Te Peng, Hui-Ling Chen, Ying Tsong Cheng, Chia Yang Shih, Min Yao Liu, Chia-Hung Chen, Chin-Feng Bioinformation Web Database In the past years, identification of alternative splicing (AS) variants has been gaining momentum. We developed AVATAR, a database for documenting AS using 5,469,433 human EST sequences and 26,159 human mRNA sequences. AVATAR contains 12000 alternative splicing sites identified by mapping ESTs and mRNAs with the whole human genome sequence. AVATAR also contains AS information for 6 eukaryotes. We mapped EST alignment information into a graph model where exons and introns are represented with vertices and edges, respectively. AVATAR can be queried using, (1) gene names, (2) number of identified AS events in a gene, (3) minimal number of ESTs supporting a splicing site, etc. as search parameters. The system provides visualized AS information for queried genes. AVAILABILITY: The database is available for free at http://avatar.iecs.fcu.edu.tw/ Biomedical Informatics Publishing Group 2005-04-22 /pmc/articles/PMC1891626/ /pubmed/17597845 Text en © 2005 Biomedical Informatics Publishing Group This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.
spellingShingle Web Database
Hsu, Fang Rong
Chang, Hwan-You
Lin, Yaw-Lin
Tsai, Yin-Te
Peng, Hui-Ling
Chen, Ying Tsong
Cheng, Chia Yang
Shih, Min Yao
Liu, Chia-Hung
Chen, Chin-Feng
AVATAR: A database for genome-wide alternative splicing event detection using large scale ESTs and mRNAs
title AVATAR: A database for genome-wide alternative splicing event detection using large scale ESTs and mRNAs
title_full AVATAR: A database for genome-wide alternative splicing event detection using large scale ESTs and mRNAs
title_fullStr AVATAR: A database for genome-wide alternative splicing event detection using large scale ESTs and mRNAs
title_full_unstemmed AVATAR: A database for genome-wide alternative splicing event detection using large scale ESTs and mRNAs
title_short AVATAR: A database for genome-wide alternative splicing event detection using large scale ESTs and mRNAs
title_sort avatar: a database for genome-wide alternative splicing event detection using large scale ests and mrnas
topic Web Database
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891626/
https://www.ncbi.nlm.nih.gov/pubmed/17597845
work_keys_str_mv AT hsufangrong avataradatabaseforgenomewidealternativesplicingeventdetectionusinglargescaleestsandmrnas
AT changhwanyou avataradatabaseforgenomewidealternativesplicingeventdetectionusinglargescaleestsandmrnas
AT linyawlin avataradatabaseforgenomewidealternativesplicingeventdetectionusinglargescaleestsandmrnas
AT tsaiyinte avataradatabaseforgenomewidealternativesplicingeventdetectionusinglargescaleestsandmrnas
AT penghuiling avataradatabaseforgenomewidealternativesplicingeventdetectionusinglargescaleestsandmrnas
AT chenyingtsong avataradatabaseforgenomewidealternativesplicingeventdetectionusinglargescaleestsandmrnas
AT chengchiayang avataradatabaseforgenomewidealternativesplicingeventdetectionusinglargescaleestsandmrnas
AT shihminyao avataradatabaseforgenomewidealternativesplicingeventdetectionusinglargescaleestsandmrnas
AT liuchiahung avataradatabaseforgenomewidealternativesplicingeventdetectionusinglargescaleestsandmrnas
AT chenchinfeng avataradatabaseforgenomewidealternativesplicingeventdetectionusinglargescaleestsandmrnas

Ejemplares similares