Rakesh Mishra's Lab in CCMB

SnS-Align (Structure and Sequence Alignment) is a tool developed in perl, used to align the protein sequences by combining sequence and structure information at an instance. Given a protein sequence of an organism, the tool is used to identify its homologue(s) in the evolutionarily distant organisms, which might not be found from either sequence alone or structure alone comparisons. A snapshot of the tool is illustrated below.

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.

RISCI – ‘Repeat Induced Sequence Changes Identifier’ - is a comprehensive, comparative genomics based, in silico subtractive hybridization tool, to identify differential insertions and associated subtle sequence changes like target site duplications (TSD), 3’ and 5' flank transductions, insertion mediated deletions, recombination mediated deletions and polymorphism induced by transposons. Post insertion changes such as recombination mediated deletions and disruptions are also picked up by RISCI. It emulates subtractive hybridization in the sense that, only when the locus in the genomes is differential, does it report the sequence changes associated with the transposon insertion.

RISCI picks up the repeat locus from a given genome (Main genome) and zooms into the orthologous locus in one or more genomes (Comparative genomes) of the same or closely related species and reports whether the insertion is differential or otherwise using a novel comparative genomics based Target site duplication finding strategy. When differential, RISCI also reports additional subtle sequence changes brought about by the transposon insertion in the main genome which may then be studied for their downstream effects. When different genomes of the same species are compared, all identified differential insertions represent polymorphic sites. RISCI also integrates the genomic context (genic or intergenic, if genic- exonic or intronic) of the the repeat locus in the main genome and of the identified orthologous locus in the comparative genome provided the annotation files are available.

RISCI.tar.gz – Perl scripts for RISCI (compatible to LINUX Operating System).

L1HS.tar.gz – Sample run of RISCI – RISCI run for L1HS full length repeats from reference human genome (Build 36.1) compared to Celera, HuRef and reference Chimpanzee genome (PanTro 2).