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Gene. 2014 Apr 10;539(1):152-3. doi: 10.1016/j.gene.2014.02.007. Epub 2014 Feb 11.

An intuitive graphical webserver for multiple-choice protein sequence search.

Author information

1
Protein Information Technology Group, Eotvos University, Pazmany Peter stny. 1/C, H-1117 Budapest, Hungary; Uratim Ltd., H-1118 Budapest, Hungary. Electronic address: banky@pitgroup.org.
2
Protein Information Technology Group, Eotvos University, Pazmany Peter stny. 1/C, H-1117 Budapest, Hungary. Electronic address: szalkai@pitgroup.org.
3
Protein Information Technology Group, Eotvos University, Pazmany Peter stny. 1/C, H-1117 Budapest, Hungary; Uratim Ltd., H-1118 Budapest, Hungary. Electronic address: grolmusz@pitgroup.org.

Abstract

Every day tens of thousands of sequence searches and sequence alignment queries are submitted to webservers. The capitalized word "BLAST" becomes a verb, describing the act of performing sequence search and alignment. However, if one needs to search for sequences that contain, for example, two hydrophobic and three polar residues at five given positions, the query formation on the most frequently used webservers will be difficult. Some servers support the formation of queries with regular expressions, but most of the users are unfamiliar with their syntax. Here we present an intuitive, easily applicable webserver, the Protein Sequence Analysis server, that allows the formation of multiple choice queries by simply drawing the residues to their positions; if more than one residue are drawn to the same position, then they will be nicely stacked on the user interface, indicating the multiple choice at the given position. This computer-game-like interface is natural and intuitive, and the coloring of the residues makes possible to form queries requiring not just certain amino acids in the given positions, but also small nonpolar, negatively charged, hydrophobic, positively charged, or polar ones. The webserver is available at http://psa.pitgroup.org.

KEYWORDS:

Multiple choice search; Protein sequence analysis; Regular expressions; Sequence analysis

PMID:
24525401
DOI:
10.1016/j.gene.2014.02.007
[Indexed for MEDLINE]

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