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Nucleic Acids Research Advance Access first published online on May 30, 2007
This version published online on May 31, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm367
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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FRalanyzer: a tool for functional analysis of fold-recognition sequence–structure alignments

Harpreet Kaur Saini* and Daniel Fischer

Computer Science and Engineering Department, 201 Bell Hall University at Buffalo, Buffalo, NY 14260, USA

*To whom correspondence should be addressed. Tel: 716 645 3180 (Ext. 163); Fax: 716 645 3464; Email: hksaini{at}cse.buffalo.edu

Received January 4, 2007. Revised April 26, 2007. Accepted April 26, 2007.

We describe FRalanyzer (Fold Recognition alignment analyzer), a new web tool to visually inspect sequence–structure alignments in order to predict functionally important residues in a query sequence of unknown function. This tool is aimed at helping to infer functional relationships between a query sequence and a template structure, and is particularly useful in analyzing fold recognition (FR) results. Because similar folds do not necessarily share the same function, it is not always straightforward to infer a function from an FR result alone. Manual inspection of the FR sequence-structure alignment is often required in order to search for conservation of functionally important residues. FRalanyzer automates parts of this time-consuming process. FRalanyzer takes as input a sequence–structure alignment, automatically searches annotated databases, displays functionally significant residues and highlights the functionally important positions that are identical in the alignment. FRalanyzer can also be used with sequence-structure alignments obtained by other methods, and with structure–structure alignments obtained from structural comparison of newly determined 3D-structures of unknown function. Fralanyzer is available at http://fralanyzer.cse.buffalo.edu/.

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