WebTraceMiner: a web service for processing and mining EST sequence trace files

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	WebTraceMiner: a web service for processing and mining EST sequence trace files
	Liang, C ; Wang, G ; Liu, L ; Ji, G ; Liu, YS ; Chen, JQ ; Webb, JS ; Reese, G ; Dean, JFD ; Ji GL(吉国力)
刊名	http://dx.doi.org/10.1093/nar/gkm299
	2007-07
关键词	MESSENGER-RNA POLYADENYLATION DATABASE TAGS
英文摘要	Expressed sequence tags (ESTs) remain a dominant approach for characterizing the protein-encoding portions of various genomes. Due to inherent deficiencies, they also present serious challenges for data quality control. Before GenBank submission, EST sequences are typically screened and trimmed of vector and adapter/linker sequences, as well as polyA/T tails. Removal of these sequences presents an obstacle for data validation of error-prone ESTs and impedes data mining of certain functional motifs, whose detection relies on accurate annotation of positional information for polyA tails added posttranscriptionally. As raw DNA sequence information is made increasingly available from public repositories, such as NCBI Trace Archive, new tools will be necessary to reanalyze and mine this data for new information. WebTraceMiner (www.conifergdb.org/software/wtm) was designed as a public sequence processing service for raw EST traces, with a focus on detection and mining of sequence features that help characterize 30 and 50 termini of cDNA inserts, including vector fragments, adapter/linker sequences, insert-flanking restriction endonuclease recognition sites and polyA or polyT tails. WebTraceMiner complements other public EST resources and should prove to be a unique tool to facilitate data validation and mining of error-prone ESTs (e. g. discovery of new functional motifs).
语种	英语
内容类型	期刊论文
源URL	[http://dspace.xmu.edu.cn/handle/2288/70697]
专题	信息技术－已发表论文
推荐引用方式 GB/T 7714	Liang, C,Wang, G,Liu, L,et al. WebTraceMiner: a web service for processing and mining EST sequence trace files[J]. http://dx.doi.org/10.1093/nar/gkm299,2007.
APA	Liang, C.,Wang, G.,Liu, L.,Ji, G.,Liu, YS.,...&吉国力.(2007).WebTraceMiner: a web service for processing and mining EST sequence trace files.http://dx.doi.org/10.1093/nar/gkm299.
MLA	Liang, C,et al."WebTraceMiner: a web service for processing and mining EST sequence trace files".http://dx.doi.org/10.1093/nar/gkm299 (2007).