27 May 2011

FASTA


AIM
         To perform local alignment for giving nucleotide (or) protein sequence using FASTA.

INTRODUCTION
         FASTA stands for Fast All reflecting the fact that it can be used for a fast protein comparison (or) a fast nucleotide comparison. This program achieve a high level of sensitivity for similarity searching at high speed. This is achieved by performing optimised structure for local alignments using a substitution matrix. The high speed of this program is achieved by using the observed pattern of word hits to identity potential matches before attempting the more time consuming optimised search. The trade of between speed and sensitivity is controlled by the K-tup parameter, which specifies the size of the word. Increasing the K-tup decreases the number of background hits. Not every word hit is investigated but instead initially looks for segments containing severalnear by hits.

TYPES OF FASTA
FAST-A3
FAST-F3
FAST-S3
FAST-X3
FAST-Y3

PROCEDURE
(1) Open the URL specified for FASTA.
(2) Choose the FASTA option given for nucleotide (or) protein.
(3) Type the required sequence in FASTA format.
(4) Select the appropriate parameters.
(5) Then click the format button and wait for few seconds.
(6) View the results and record the first five hits as observation.

URL: www.ebi.ac.uk/fasta







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