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

Harpreet Kaur Saini, Daniel Fischer

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

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 sequencestructure 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/.

Original languageEnglish
Pages (from-to)W499-W502
JournalNucleic Acids Research
Volume35
Issue numberSUPPL.2
DOIs
StatePublished - 1 Jul 2007
Externally publishedYes

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