Nucleic Acids Research Advance Access originally published online on May 8, 2007
Nucleic Acids Research 2007 35(Web Server issue):W137-W142; doi:10.1093/nar/gkm299
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W137-W142
© 2007 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.
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WebTraceMiner: a web service for processing and mining EST sequence trace files
1Department of Botany, Miami University, Oxford, Ohio 45056, USA, 2Department of Automation, Xiamen University, Xiamen, Fujian, 361005, China, 3Research Computing Support Group, Miami University, Oxford, Ohio 45056, USA and 4Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602, USA
*To whom correspondence should be addressed. Tel: +1 513 529 2336; Fax: +1 513 529 4243; Email: liangc{at}muohio.edu
Received January 9, 2007. Revised March 30, 2007. Accepted April 14, 2007.
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 3' and 5' 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).
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