dorsal/arxiv
View SchemaPFMFind: a system for discovery of peptide homology and function
| Authors | Aleksandar Stojmirović, Peter Andreae, Mike Boland, Thomas William Jordan, Vladimir G. Pestov |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0603011 |
| URL | https://arxiv.org/abs/q-bio/0603011 |
| License | http://creativecommons.org/licenses/publicdomain/ |
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 score matrices and PSSMs obtained through an iterative procedure similar to PSI-BLAST. PSSM construction is customisable through plugins written in Python. PFMFind consists of a GUI client, an algorithm using an index for fast similarity search and a relational database for storing search results and sequence annotations. It is written mostly in Python. All components communicate between themselves using TCP/IP sockets and can be located on different physical machines.
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"date_created": "2026-03-02T18:01:35.648000Z",
"date_modified": "2026-03-02T18:01:35.648000Z",
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"abstract": "Protein Fragment Motif Finder (PFMFind) is a system that enables efficient\ndiscovery of relationships between short fragments of protein sequences using\nsimilarity search. It supports queries based on score matrices and PSSMs\nobtained through an iterative procedure similar to PSI-BLAST. PSSM construction\nis customisable through plugins written in Python. PFMFind consists of a GUI\nclient, an algorithm using an index for fast similarity search and a relational\ndatabase for storing search results and sequence annotations. It is written\nmostly in Python. All components communicate between themselves using TCP/IP\nsockets and can be located on different physical machines.",
"arxiv_id": "q-bio/0603011",
"authors": [
"Aleksandar Stojmirovi\u0107",
"Peter Andreae",
"Mike Boland",
"Thomas William Jordan",
"Vladimir G. Pestov"
],
"categories": [
"q-bio.QM",
"q-bio.GN"
],
"license": "http://creativecommons.org/licenses/publicdomain/",
"title": "PFMFind: a system for discovery of peptide homology and function",
"url": "https://arxiv.org/abs/q-bio/0603011"
},
"schema_id": "dorsal/arxiv",
"source": {
"execution_id": "3b2ba4f9-a15b-4b49-8dc6-ac6a08715d1a",
"id": "arXiv Dataset IDs",
"type": "Model",
"variant": "snapshot-2026-03-01",
"version": "0.1.0"
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