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WISA is a short name given to Web Interface for Sequence Alignment.This is a tool which perform various types of alignment.
Three types of dynamic alignment can be performed by this tool are global alignment,local alignment and end space free alignment (semi-global alignment). This type of alignment can be performed for both types of sequences i.e. protein sequences and nucleotide sequence(s).For the protein sequence alignment a user can use either of the two scoring matrices PAM or BLOSUM. For the nucleotide sequence alignment a user can define the values of identity,transition,transversion,gap opening and gap penalty as required.
It will also look for homologous sequences using various standard methds and options availabe through BLAST.
It can also look for MSA (Multiple Sequence Alignment) for protein sequences using various scoring matrices. Profile based method has been implemented for generating MSA. A profile matrix will be generated which will further be used to generate Newick format phylogenetic tree. This tree can be visualized in any standard tree viewer.
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