Title

PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition

UMMS Affiliation

Department of Cell and Developmental Biology; Wellstone Center for FSHD

Date

9-1-2014

Document Type

Article

Medical Subject Headings

Algorithms; Amino Acids; Internet; Prions; Saccharomyces cerevisiae Proteins; Sequence Analysis, Protein; *Software

Disciplines

Biochemistry, Biophysics, and Structural Biology | Bioinformatics | Molecular Biology

Abstract

Prions are self-templating protein aggregates that stably perpetuate distinct biological states and are of keen interest to researchers in both evolutionary and biomedical science. The best understood prions are from yeast and have a prion-forming domain with strongly biased amino acid composition, most notably enriched for Q or N. PLAAC is a web application that scans protein sequences for domains with P: rion- L: ike A: mino A: cid C: omposition. Users can upload sequence files, or paste sequences directly into a textbox. PLAAC ranks the input sequences by several summary scores and allows scores along sequences to be visualized. Text output files can be downloaded for further analyses, and visualizations saved in PDF and PNG formats.

AVAILABILITY AND IMPLEMENTATION: http://plaac.wi.mit.edu/. The Ruby-based web framework and the command-line software (implemented in Java, with visualization routines in R) are available at http://github.com/whitehead/plaac under the MIT license. All software can be run under OS X, Windows and Unix.

Rights and Permissions

Citation: Bioinformatics. 2014 Sep 1;30(17):2501-2. doi: 10.1093/bioinformatics/btu310. Epub 2014 May 13. Link to article on publisher's site

Related Resources

Link to Article in PubMed

PubMed ID

24825614