WebGMAP: a web service for mapping and aligning cDNA sequences to genomes

CORC > 厦门大学 > 信息技术－已发表论文

	WebGMAP: a web service for mapping and aligning cDNA sequences to genomes
	Liang, C. ; Liu, L. ; Ji, G. L. ; Ji GL(吉国力)
刊名	http://dx.doi.org/10.1093/nar/gkp389
	2009-07-01
关键词	MESSENGER-RNA ALIGNMENT ANNOTATION DATABASE PROJECT PROGRAM PLANTS TAGS TOOL
英文摘要	Miami University; Ohio Plant Biotechnology Consortium; National Natural Science Fund of China [60774033]; Natural Science Foundation of Fujian Province in China [B0710031]; Specialized Research Fund for the Doctoral Program of Higher Education [2007038400; 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.
语种	英语
内容类型	期刊论文
源URL	[http://dspace.xmu.edu.cn/handle/2288/70696]
专题	信息技术－已发表论文
推荐引用方式 GB/T 7714	Liang, C.,Liu, L.,Ji, G. L.,et al. WebGMAP: a web service for mapping and aligning cDNA sequences to genomes[J]. http://dx.doi.org/10.1093/nar/gkp389,2009.
APA	Liang, C.,Liu, L.,Ji, G. L.,&吉国力.(2009).WebGMAP: a web service for mapping and aligning cDNA sequences to genomes.http://dx.doi.org/10.1093/nar/gkp389.
MLA	Liang, C.,et al."WebGMAP: a web service for mapping and aligning cDNA sequences to genomes".http://dx.doi.org/10.1093/nar/gkp389 (2009).