WebTraceMiner: a web service for processing and mining EST sequence trace files.
Nucleic Acids Res
; 35(Web Server issue): W137-42, 2007 Jul.
Article
in En
| MEDLINE
| ID: mdl-17488839
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).
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Software
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Sequence Alignment
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Sequence Analysis, DNA
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DNA, Complementary
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Computational Biology
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Expressed Sequence Tags
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Gene Expression Profiling
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Databases, Genetic
Limits:
Animals
Language:
En
Journal:
Nucleic Acids Res
Year:
2007
Document type:
Article
Affiliation country: