Nucleic Acids Research Advance Access originally published online on May 22, 2009
Nucleic Acids Research 2009 37(Web Server issue):W77-W83; doi:10.1093/nar/gkp389
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W77-W83
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Articles |
WebGMAP: a web service for mapping and aligning cDNA sequences to genomes
1Department of Botany, 2Department of Computer Science and Systems Analysis, Miami University, Oxford, OH 45056, USA and 3Department of Automation, Xiamen University, Xiamen, Fujian 361005, China
*To whom correspondence should be addressed. Tel: +1 513 529 2336; Fax: +1 513 529 4243; Email: liangc{at}muohio.edu
Received February 28, 2009. Revised April 15, 2009. Accepted April 29, 2009.
The genomes of thousands of organisms are being sequenced, often with accompanying sequences of cDNAs or ESTs. One of the great challenges in bioinformatics is to make these genomic sequences and genome annotations accessible in a user-friendly manner to general biologists to address interesting biological questions. We have created an open-access web service called WebGMAP (http://www.bioinfolab.org/software/webgmap) that seamlessly integrates cDNA-genome alignment tools, such as GMAP, with easy-to-use data visualization and mining tools. This web service is intended to facilitate community efforts in improving genome annotation, determining accurate gene structures and their variations, and exploring important biological processes such as alternative splicing and alternative polyadenylation. For routine sequence analysis, WebGMAP provides a web-based sequence viewer with many useful functions, including nucleotide positioning, six-frame translations, sequence reverse complementation, and imperfect motif detection and alignment. WebGMAP also provides users with the ability to sort, filter and search for individual cDNA sequences and cDNA-genome alignments. Our EST-Genome-Browser can display annotated gene structures and cDNA-genome alignments at scales from 100 to 50 000 nt. With its ability to highlight base differences between query cDNAs and the genome, our EST-Genome-Browser allows biologists to discover potential point or insertion-deletion variations from cDNA-genome alignments.