Subject:- Bioinformatics
FASTA Programs and Algorithm
FASTA Programs
FASTA: Compares the protein sequence to another protein sequence in a
database or compares nucleotide sequence to another nucleotide sequence
in a database.
FASTX, FASTY: It performs a search for comparing the nucleotide sequence
to a protein sequence database.
SSEARCH: It performs a Smith-Watermann alignment, between a protein
sequence and another protein sequence/nucleotide sequence and another
nucleotide sequence. It is local alignment.
GGSEARCH: Compares a protein or DNA sequence to a sequence database
using Global alignment. It compares the query sequences that are between
80% of the length of the query.
GLSEARCH: Compares a protein or DNA sequence to a sequence in a
database. The alignments are global in query and local in database.
Parameters used in FASTA algorithm :
Threshold: It is a boundary of minimum or maximum value which can be
used to filter out words during comparison.
True Homology: In FASTA true homology refers how much the sequence is
similar to the query sequence.
E-value: It decreases exponentially with the score that is assigned to an
alignment between two sequences.
Putative conserved domains: These are the domains that have different
functionalities.
Working of FASTA algorithm :
•Nucleotide or protein sequence is taken as input.
• The speed and sensitivity is controlled by the parameter called ktup,
which specifies the size of the word. This program uses the word hits
to identify potential matches between the query sequence and
database sequence. Lesser the ktup value,more sensitive the search.
By default ktup is 2 for proteins and ktup is 4 or 6 for nucleotides,
initially it checks for segment’s containing several nearby hits.
•Then it finds the similar local regions based on the matches and
mismatches (scoring) and isolate thehighest matches from the
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