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FASTA

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41 views24 pages

FASTA

Study documents

Uploaded by

tanzeela iftikhar
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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FASTA

(Fast Adaptive Shrinkage Threshold Algorithm)

Course code: BNB-422


Credit hours: 3(2-1)
Dr. Farheen Bhatti
Bioinformatics

Research, development,
application of computational tools
and approaches for expanding
the use of biological, including
those to acquire, store, organize,
analyze such data.
Similarity search tools

• Computer softwares containing an organized


body of sequence of nucleic acid & proteins &
designed to update, query & retrieve the data.

• They contain amino acid sequences of proteins


& nucleotide sequence of nucleic acid.

• Find out similarities between the query


sequence & data in database are called
database similarity search tools.
FASTA
In bioinformatics and biochemistry,
the FASTA format is a text-based
format for representing either
nucleotide sequences or amino acid
sequences, in which nucleotides or
amino acids are represented using
single-letter codes. The format
allows for sequence names and
comments to precede the
sequences.
FASTA
• FASTA package was 1st described as
by Lipman & Pearson in 1985.
• FASTA is a DNA & protein sequence
alignment software.
• FASTA is a fast HOMOLOGY search
tool.
• Similar to BLAST , but this tool will
speed up sequence comparison when
compared with BLAST.
• Hence it is called FASTA.
Cntd…
• FAST-P stands for protein , compare the
amino acid sequence of proteins &
FAST-N stands for nucleotide alignment ,
compare the nucleotide sequence of
DNA.
• It is Bioinformatic tool.
• It is biological database.
• It compare the amino acid sequence of
different proteins or the nucleotide
sequence of different DNA.
FASTA Format

• Header line which begins with ‘>’ gives


a unique identifier for the sequence.
• The gap character ‘-’ is found in
locations corresponding to gaps in the
sequence.
• E.g.
>JC2395 NVSDVNLNK---
YIWRTAEKMK---QKIQLLQWYQSHGKT
Amino acid code Meaning
A Alanine
B Asparagine
C Cysteine
D Aspartic acid
E Glutamic acid
F Phenylalanine
G Glycine
H Histidine
I Isoleucine
J Leucine (L)
K Lysine
L Leucine
M Methionine
N Asparagine
O Pyrrolysine
Amino acid code Meaning
P Proline
Q Glutamine
R Arginine
S Serine
T Threosine
U Selenocysteine
V Valine
W Tryptophan
Y Tyrosine
Z Glutamic acid (E)
FASTA Programs

• FASTA - compares a query protein sequence to


a protein library or DNA sequence to a DNA
library.
• TFASTA – compares a query sequence to a DNA
library, after the DNA sequence has been
translated in all 6 reading frames.
• FASTS – compares a set of ordered peptide
fragments, obtained from mass-spectrometry
analysis of a protein against a protein database.
• FASTX & Y – compares a query DNA sequence
to a protein sequence database , translating the
DNA sequence in all 6 reading frames.
salient features of fasta

• FASTA find out patches of sequence


SIMILARITY between the query and
database.
• FASTA may contain GAPS.
• FASTA is RAPID.
• FASTA is working on the basis of
FASTA algorithm developed by Fredi
and Barton.
Cntd…

• Programs can be run locally or by


sending query sequence to the FASTA
Email serer.
• Program achieve a high level of
sensitivity for similarity search at high
speed.
• FASTA is not guaranteed to find best
alignment between the query and
database.
uses of fasta

• Identification of species.
• Establishing phylogeny.
• DNA mapping.
• Understanding biochemical
functions of protein.
• Studying evolution of species.
• Identification of mutations.
• Calculating molecular weight.
Cntd…
• Studying atomic composition.
• Knowing amino acid composition.
• Identification of specific function of
sequence.
• Comparison of DNAs.

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