The Profile Comparer (PRC,
Martin Madera) is a program for aligning and scoring profile
hidden Markov models.
Here, you can input your query alignment and run PRC against profile HMM libraries of domain databases.
Your input alignment can be in
(aligned) FASTA,
ClustalW,
Stockholm,
SELEX
or GCG MSF format.
Using webPRC you can identify and evaluate similar alignments in Pfam,
CATH, NCBI's Conserved Domain Database (CDD)
TIGRFAMs and
SUPERFAMILY,
both in HMM and alignment space.
Additionally, you can produce logos, and view or download the multiple sequence alignments corresponding to the hits.
Documentation: introduction to the PRC web server, including
example output.
You can also rerun the example.
References:
Brandt B.W. and Heringa J. (2009) webPRC: webPRC: the Profile Comparer for alignment-based searching of public domain databases.
Nucleic Acids Research 37:W48-W52.
Madera M. PRC, the Profile Comparer (we use version 1.5.5 August 2008).
Madera M. (2008) Profile Comparer: a program for scoring and aligning profile hidden Markov models.
Bioinformatics 24:2630-2631.
Visualization:
Two Sample Logo: Vacic V., Iakoucheva L.M., Radivojac P. (2006) Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments.
Bioinformatics 22:1536-1537.
HMM-Logo: Schuster-Böckler B., Schultz J., Rahmann S. (2004) HMM Logos for visualization of protein families.
BMC Bioinformatics 5:7.
Jalview: Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004)
The Jalview Java Alignment Editor.
Bioinformatics 20:426-427.
Databases:
CATH: Cuff, A.L., Sillitoe, I., Lewis, T., Redfern, O.C., Garratt, R., Thornton, J. and Orengo, C.A. (2009)
The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies.
Nucleic Acids Research 37: D310-314.
CDD: Marchler-Bauer, A., Anderson, J.B., Chitsaz, F., Derbyshire, M.K., DeWeese-Scott, C., Fong, J.H.,
Geer, L.Y., Geer, R.C., Gonzales, N.R., Gwadz, M. et al. (2009)
CDD: specific functional annotation with the Conserved Domain Database.
Nucleic Acids Research 37: D205-210.
KOG: Koonin, E.V., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Krylov, D.M., Makarova, K.S.,
Mazumder, R., Mekhedov, S.L., Nikolskaya, A.N., Rao, B.S. et al. (2004)
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes.
Genome Biology 5: R7.
Pfam: Finn, R.D.,Tate, J., Mistry, J., Coggill, P.C., Sammut, J.S., Hotz,H.R., Ceric, G., Forslund, K., Eddy, S.R., Sonnhammer, E.L. and Bateman A. (2008)
The Pfam protein families database:
Nucleic Acids Research 36: D281-D288.
TIGRFAMs: Selengut, J.D., Haft, D.H., Davidsen, T., Ganapathy, A., Gwinn-Giglio, M., Nelson, W.C.,
Richter, A.R. and White, O. (2007)
TIGRFAMs and Genome Properties: tools for the assignment
of molecular function and biological process in prokaryotic genomes.
Nucleic Acids Research 35: D260-264.
SUPERFAMILY: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001)
Assignment of Homology to Genome Sequences using a Library of
Hidden Markov Models that Represent all Proteins of Known Structure.
Journal of Molecular Biology 313: 903-919.
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