SnS-Align [A graphic tool for alignment of distantly related proteins]

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SnS-Align (Structure and Sequence Alignment) is a tool developed in perl, which is used to align the protein sequences by combining sequence and structure information at an instance (the sanwiched sequence). The amino acids corresponding to Secondary structural elements (a-Helices and b-Sheets) in the primary protein sequence are replaced by characters designated for a-Helices and b-Sheets respectively. This leaves amino acid sequences only in the regions where there are no a-Helices or b-Sheets. we term this representation of protein sequence as sandwiched sequence.

Given a protein or genomic sequence of an organism, the tool is used to identify its homologue(s) in the target database (proteins of distant organisms), which might not be found from either sequence alone or structure alone comparisons. Query should be a FASTA formatted protein sequence file. DB (Database) is a set of mutliple protein sequences in FASTA format. You can see the SnS-algnment in a Graphical User interface. *(star) indicates the conservation of secondary structure and + (plus) indicates the conservation of sequence. You can save the alignment in Text format or Post script format by selecting the save alignment option. The summary of the alignments containing similarity and score can also be saved in a text format. A snapshot of the tool is illustrated below.

Requirements

• Perl is to be installed with the Tk module (use Active-Perl for windows and for linux get your rpm for the Tk module)
• EMBOSS is to be installed to run the program (EMBOSS for Windows and Linux is freely available)

Download

        SnS-Align is available for Windows and Linux. SnS is not tested on Mac, but if you are interested to use please don't hesitate to contact for any support.

Supplementary Data

SnS-Align is tested using the gap junction protein superfamily (innexins/pannexins) and the classic myoglobin family. The divergence information of the myoglobin proteins used can be obtained here

For further queries contact gmanyam[AT]gmu.edu