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BLAST

BLAST, or Basic Local Alignment Search Tool, is a bioinformatics algorithm developed by Stephen Altschul in 1990 for comparing biological sequences, such as proteins and nucleotides, to identify similarities. It operates by breaking down query sequences into fragments and searching a database for matches, offering various types including BLASTn and BLASTp for nucleotide and protein comparisons, respectively. Key features include accessibility, speed, flexibility, and a user-friendly interface, making it a crucial tool for researchers in genomics and molecular biology.

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4 views

BLAST

BLAST, or Basic Local Alignment Search Tool, is a bioinformatics algorithm developed by Stephen Altschul in 1990 for comparing biological sequences, such as proteins and nucleotides, to identify similarities. It operates by breaking down query sequences into fragments and searching a database for matches, offering various types including BLASTn and BLASTp for nucleotide and protein comparisons, respectively. Key features include accessibility, speed, flexibility, and a user-friendly interface, making it a crucial tool for researchers in genomics and molecular biology.

Uploaded by

ankita soreng.
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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BLAST

INTRODUCTION
➢ BLAST STANDS FOR BASIC LOCAL ALIGNMENT SEARCH TOOL
➢ IT WAS DEVELOPED BY STEPHEN ALTSCHUL IN 1990.
➢ IN BIOINFROMATIC BLAST IS AN ALGORITHM AND PROGRAM FOR
COMPARING PRIMARY BIOLOGICAL SEQUENCE INFORMATION.
➢ IT IS A SEQUENCE SIMILARITY SEARCH PROGRAM THAT IS USED TO COMPARE
QUERY SEQUENCE WITH SEQUENCE DATABASE AND FIND SIMILARITY BETWEEN
THEM.
➢ SUCH AS AMINO –ACID SEQUENCE OF PROTEIN OR THE NUCLEOTIDES OF
DNA AND OR RNA SEQUENCE
 A BLAST SEARCH ENABLES A RESEARCHER TO COMPARE A PROTEIN OR NUCLEOTIDE
SEQUENCE CALLED QUERY.WITH A LIBRARY OR DATABASE OF SEQUENCE ,AND IDENTIFY
DATABASE SEQUENCE THAT RESEMBLES THE QUERY SEQUENCE .
 IT BREAKS THE QUERY AND DATABASE SEQUENCE INTO FRAGMENTS AND SEEKS MATCHES
BETWEEN THEM.
 EXAMPLE – GENE OF MOUSE ,A SCIENTIST WILL TYPICALLY PERFORM A BLAST SEARCH OF
THE HUMAN GENOME TO SEE IF HUMAN CARRY A SIMILAR GENE.BLAST WILL IDENTIFY
SEQUENCE IN THE HUMAN GENOME THAT RESEMBLES THE MOUSE GENE BASED ON
SIMILARITY OF SEQUENCE .
 BLAST IS A COMPUTER ALGORITHM THAT IS AVAILABLE FOR USE ONLINE AT NCBI WEBSITE.
 THE MOST COMMON USED TOOL TO EXAMINE DNA AND PROTEIN SEQUENCE IS ALSO
KNOWN AS BLAST.
TYPES OF BLAST

 BLASTn :- Compares nucleotide query sequences to a nucleotide


sequence or a database of nucleotide sequences.
 BLASTp :- Compares one or more protein query sequences to a subject
protein sequences or a database of protein sequences.
 BLASTx :- Compares a nucleotide query sequences (translated in protein
sequences) against a database of protein sequences.
 tBLASTn :- Compares a protein query sequences against the six frame
translation of a database of nucleotide sequences.
 tBLASTx :- Compares the translated nucleotide sequences against the
translated nucleotide sequence database.
CHARACTERSTICS OF BLAST
Several key features of BLAST make it a widely used tool in bioinformatics some of these
are as follows:-
 Accessibility – BLAST is accessible to research over the internet.
 Fast and efficient – BLAST is a fast and efficient, making it possible to handle large
database of sequences.
 Flexible and versatile – It is flexible and versatile tool as it can be used to search for
similarities in both nucleotide and protein sequences.
 High sensitivity – it is highly sensitive which allows the identification of even small
similarities between sequences.
 Region of local similarities – it aims to identify regions of local similarities between the
query sequences and the database sequences rather than attempting to align the
local sequences.
 User friendly interface – It has a user friendly interface that makes it easy to input query
sequences and interpret the result.
 Answer questions – BLASt can answer questions that would be difficult to answer in a
lab or in the field.
HOW BLAST WORKS
 work of blast is comparing query sequence with database sequence so that we can find
the similarity reason is present or not.
 It performs sequence alignment by following some steps:-
Step 1 - Creates a look up table
When we put query sequence into blast then these query sequences are break down
into segments
Example -proteins have 3amino acid segment
Nucleotide have 11 nucleotide segment
•these segments are called as WORDS.
•SEEDING-The process of finding similar sequence is Called seeding .

Step 2 - Search a database of known sequences


Step 3 - scores the similarity of the matching words.

•to provide the scores their is substitution matrics is present

Example - protein sequence - a) PAM(point or percentage acceptance mutation)


b) BLOSUM

Step 4 - After providing scores , pair wise alignment is started by BLAST

•extension of WORDS can be done from both direction

Step 5 - BLAST calculate some statistical significance values

•E-Value(expect value)
•E-value is low , level of significance is high
How to run NCBI BLAST
 Go to the NCBI homepage and select BLAST
 Select the type of Blast.
- Select nucleotide BLAST for comparing an unknown nucleotide sequence to known
nucleotide sequence.
- Select protein BLAST for comparing an unknown protein sequence to Known protein
sequences.
 Enterthe query sequence
In the search box
 Provide a job tittle
 Choose a database to
query
 Click BLAST
READING BLAST REPORT
SUMMARY SECTION
 Job title – shows the title given by the
user.
 NID – shows the unique identifier to this
search for sharing and problem
reporting.
 Program – list the search conducted,
BLASTn in this case.
 Database – shows the name of target
database searched
 Query id – it is the query’ sequence id
for which the result is shown.
 Description – it is the title of the query
sequence from its FASTA defline
 Molecular type – shows the type of
sequence
 Query length – shows the length of
query sequence
DESCRIPTION SECTION

The description tab contains a summary


table of hits found by BLAST. It is the
default tab shown.
GRAPHIC SUMMARY SECTION

Graphic summary is a
graphical
representation of
alignments between a
query sequence and
the database
sequence.
DISTANCE TREE OF RESULT

It presents the matches in


a distance tree format
TAXONOMY SECTION

This displays the


taxonomic distribution
of matched subject
sequence in the
database
ALIGNMENTS SECTION

It contains the detailed


pairwise alignments
between query and the
database sequence
Max[imum] Score : the highest alignment score calculated from the sum
of the rewards for matched nucleotides and penalties for mismatches and
gaps.
Total Score: the sum of alignment scores of all segments from the same
subject sequence.
Query Cover[age]: the percent of the query length that is included in the
aligned segments.
E[xpect] Value: the number of alignments expected by chance with the
calculated score or better. The expect value is the default sorting metric;
for significant alignments the E value should be very close to zero.
Ident[ity]: the highest percent identity for a set of aligned segments to the
same subject sequence.
Acc[ession] Len[gth] : the number of nucleotides or amino acids in the
result sequence identified by the accession number
Accession [number]: a unique identifier assigned to records in the NCBI
databases
USES OF BLAST
 Predicts protein and gene functions :- BLAST can help predict the functions of
genes and proteins in whole genomes.
 Identify species :- BLAST can help identify the correct species or homologous
species when sequencing DNA from unknown species.
 Identify evolutionary relationships :- BLAST can help identify evolutionary
relatedness between sequences, also known as homology.
 Map DNA to a chromosome :- BLAST can help show the position of query
sequences in studies of genetic diseases.
 Compare Protein Sequences :- BLAST can use to compare affected protein
sequences in the studies of genetic diseases.
 Design primers :- BLAST can be used to design primers to amplify a gene region
of interest from biological samples.

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