# FASTA Programs and Algorithm – Subject:- Bioinformatics FASTA Programs and Algorithm FASTA Programs

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