title: ProteinParser--a community based tool for the generation of a detailed protein consensus and FASTA output.
abstract: Comparison of bioinformatic data is a common application in the life sciences and beyond. In this communication, a novel Java based software tool, ProteinParser, is outlined. This software tool calculates a detailed consensus, or most common, amino acid at a given position in an aligned protein set, whilst also generating a full consensus protein FASTA output. A second application of this software tool, computing a consensus amino acid given a tolerance threshold, is also demonstrated. The phytase and the common bacterial beta-lactamase proteins are analysed as 'proof of concept' examples. Consensus proteins, as generated by ProteinParser, are regularly utilised in the selection of residues for protein stabilisation mutagenesis; however, this widely applicable software tool will find many alternative applications in areas such as protein homology modelling.
authors.affiliation: School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland. Barry.Ryan5@mail.dcu.ie
authors.forename: Barry J
authors.initials: BJ
authors.lastname: Ryan
authors.forename: Ronan
authors.initials: R
authors.lastname: Barrett
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D011506:Proteins