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


METHODS
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.
Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Department of Pathology, Beth Israel Deaconess Medical Center, Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA, Department of Biology, Howard Hughes Medical Institute, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139 and Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Department of Pathology, Beth Israel Deaconess Medical Center, Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA, Department of Biology, Howard Hughes Medical Institute, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139 and Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Department of Pathology, Beth Israel Deaconess Medical Center, Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA, Department of Biology, Howard Hughes Medical Institute, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139 and Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
Alex K
AK
Lancaster
Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Department of Pathology, Beth Israel Deaconess Medical Center, Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA, Department of Biology, Howard Hughes Medical Institute, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139 and Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
Andrew
A
Nutter-Upham
Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Department of Pathology, Beth Israel Deaconess Medical Center, Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA, Department of Biology, Howard Hughes Medical Institute, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139 and Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Department of Pathology, Beth Israel Deaconess Medical Center, Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA, Department of Biology, Howard Hughes Medical Institute, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139 and Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Department of Pathology, Beth Israel Deaconess Medical Center, Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA, Department of Biology, Howard Hughes Medical Institute, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139 and Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
Susan
S
Lindquist
Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Department of Pathology, Beth Israel Deaconess Medical Center, Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA, Department of Biology, Howard Hughes Medical Institute, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139 and Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
Oliver D
OD
King
D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D020407:Internet; D011328:Prions / Q000737:chemistry*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry; D020539:Sequence Analysis, Protein; D012984:Software
D000596:Amino Acids; D011328:Prions; D029701:Saccharomyces cerevisiae Proteins