SeqScrub: a web tool for automatic cleaning and annotation of FASTA file headers for bioinformatic applications

Abstract

Data consistency is necessary for effective bioinformatic analysis. SeqScrub is a web tool that parses and maintains consistent information about protein and DNA sequences in FASTA file format, checks if records are current, and adds taxonomic information by matching identifiers against entries in authoritative biological sequence databases. SeqScrub provides a powerful, yet simple workflow for managing, enriching and exchanging data, which is crucial to establish a record of provenance for sequences found from broad and varied searches; for example, using BLAST on continually updated genome sequence sets. Headers standardized using SeqScrub can be parsed by a majority of bioinformatic tools, stay uniformly named between collaborators and contain informative labels to aid management of reproducible, scientific data.

SeqScrub is available at http://bioinf.scmb.uq.edu.au/seqscrub

METHOD SUMMARY

SeqScrub is a web tool that takes a set of biological sequences in FASTA format and allows the user to: 1) ‘scrub’ files by removing unnecessary information from the sequence identifier such as characters and spaces that can cause input errors in bioinformatic tools; 2) check that sequences are not obsolete; and 3) annotate a sequence's taxonomic information onto the header.