Abstract
Protein Fragment Motif Finder (PFMFind) is a system that enables efficient discovery of relationships between short fragments of protein sequences using similarity search. It supports queries based on amino acid similarity matrices and position specific score matrices (PSSMs) obtained through an iterative procedure. PSSM construction is customisable through plugins written in Python. PFMFind consists of a GUI client, an index for fast similarity search and a relational database for storing search results and sequence annotations. It is written mostly in Python. The components of PFMFind communicate through TCP/IP sockets and can be located on different physical machines. PFMFind is freely available for download (under a GPL licence) from http://pfmfind.stojmirovic.org .
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References
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped BLAST and PSI–BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997)
Bairoch, A., Apweiler, R., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M.J., Natale, D.A., O’Donovan, C., Redaschi, N., Yeh, L.S.L.: The Universal Protein Resource (UniProt). Nucleic Acids Res 33 Database Issue, 154–159 (2005)
Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C.: A model of evolutionary change in proteins. In: Dayhoff, M.O. (ed.) Atlas of Protein Sequence and Structure, vol. 5, ch.22, pp. 345–352. National Biomedical Research Foundation (1978)
Gribskov, M., McLachlan, A.D., Eisenberg, D.: Profile analysis: detection of distantly related proteins. Proc Natl. Acad. Sci. USA 84, 4355–4358 (1987)
Henikoff, S., Henikoff, J.G.: Position-based sequence weights. J. Mol. Biol. 243(4), 574–578 (1994)
Henikoff, S., Henikoff, J.G.: Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89, 10915–10919 (1992)
Hunter, S., Jones, P., Mitchell, A., Apweiler, R., Attwood, T.K., Bateman, A., Bernard, T., Binns, D., Bork, P., Burge, S., de Castro, E., Coggill, P., Corbett, M., Das, U., Daugherty, L., Duquenne, L., Finn, R.D., Fraser, M., Gough, J., Haft, D., Hulo, N., Kahn, D., Kelly, E., Letunic, I., Lonsdale, D., Lopez, R., Madera, M., Maslen, J., McAnulla, C., McDowall, J., McMenamin, C., Mi, H., Mutowo-Muellenet, P., Mulder, N., Natale, D., Orengo, C., Pesseat, S., Punta, M., Quinn, A.F., Rivoire, C., Sangrador-Vegas, A., Selengut, J.D., Sigrist, C.J.A., Scheremetjew, M., Tate, J., Thimmajanarthanan, M., Thomas, P.D., Wu, C.H., Yeats, C., Yong, S.Y.: Interpro in 2011: New developments in the family and domain prediction database. Nucleic Acids Res. 40(Database issue), D306–D312 (2012)
Pestov, V., Stojmirović, A.: Indexing schemes for similarity search: an illustrated paradigm. Fundam. Inform. 70(4), 367–385 (2006)
Sjölander, K., Karplus, K., Brown, M., Hughey, R., Krogh, A., Mian, I., Haussler, D.: Dirichlet mixtures: A method for improving detection of weak but significant protein sequence homology. Comput. Appl. Biosci. 12(4), 327–345 (1996)
Stojmirović, A., Pestov, V.: Indexing schemes for similarity search in datasets of short protein fragments. Inf. Syst. 32(8), 1145–1165 (2007)
Watt, T.J., Doyle, D.F.: ESPSearch: a program for finding exact sequences and patterns in DNA, RNA, or protein. Biotechniques 38(1), 109–115 (2005)
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Stojmirović, A., Andreae, P., Boland, M., Jordan, T.W., Pestov, V.G. (2013). PFMFind: A System for Discovery of Peptide Homology and Function. In: Brisaboa, N., Pedreira, O., Zezula, P. (eds) Similarity Search and Applications. SISAP 2013. Lecture Notes in Computer Science, vol 8199. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-41062-8_32
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DOI: https://doi.org/10.1007/978-3-642-41062-8_32
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