title: WebTraceMiner: a web service for processing and mining EST sequence trace files.
abstract: 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).
authors.affiliation: Department of Botany, Miami University, Oxford, Ohio 45056, USA. liangc@muohio.edu
authors.forename: Chun
authors.initials: C
authors.lastname: Liang
authors.forename: Gang
authors.initials: G
authors.lastname: Wang
authors.forename: Lin
authors.initials: L
authors.lastname: Liu
authors.forename: Guoli
authors.initials: G
authors.lastname: Ji
authors.forename: Yuansheng
authors.initials: Y
authors.lastname: Liu
authors.forename: Jinqiao
authors.initials: J
authors.lastname: Chen
authors.forename: Jason S
authors.initials: JS
authors.lastname: Webb
authors.forename: Greg
authors.initials: G
authors.lastname: Reese
authors.forename: Jeffrey F D
authors.initials: JF
authors.lastname: Dean
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D018076:DNA, Complementary / Q000737:chemistry* / Q000235:genetics*; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling / Q000379:methods*; D020407:Internet; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D018076:DNA, Complementary