Abstract:
:Well defined biomacromolecular patterns such as binding sites, catalytic sites, specific protein or nucleic acid sequences, etc. precisely modulate many important biological phenomena. We introduce PatternQuery, a web-based application designed for detection and fast extraction of such patterns. The application uses a unique query language with Python-like syntax to define the patterns that will be extracted from datasets provided by the user, or from the entire Protein Data Bank (PDB). Moreover, the database-wide search can be restricted using a variety of criteria, such as PDB ID, resolution, and organism of origin, to provide only relevant data. The extraction generally takes a few seconds for several hundreds of entries, up to approximately one hour for the whole PDB. The detected patterns are made available for download to enable further processing, as well as presented in a clear tabular and graphical form directly in the browser. The unique design of the language and the provided service could pave the way towards novel PDB-wide analyses, which were either difficult or unfeasible in the past. The application is available free of charge at http://ncbr.muni.cz/PatternQuery.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Sehnal D,Pravda L,Svobodová Vařeková R,Ionescu CM,Koča Jdoi
10.1093/nar/gkv561subject
Has Abstractpub_date
2015-07-01 00:00:00pages
W383-8issue
W1eissn
0305-1048issn
1362-4962pii
gkv561journal_volume
43pub_type
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