Bioinformatics involves the analysis of biological information using computers and statistical techniques, In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. The sequence alignment is made between a known sequence and unknown sequence or between two unknown sequences. The known sequence is called reference sequence. The unknown sequence is called query sequence . BLAST stands for Basic Local Alignment Search Tool. It addresses a fundamental problem in bioinformatics research. BLAST tool is used to compare a query sequence with a library or database of sequences. In Bioinformatics, is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences. BLAST was developed by stochastic model of Samuel Karlin and Stephen Altschul  in 1990. They proposed “a method for estimating similarities between the known DNA sequence of one organism with that of another”. A BLAST search enables a researcher to compare a subject protein or nucleotide sequence (called a query sequence) with a library or database of sequences and identify database sequences that resemble the query sequence above a certain threshold.

1. RANI DURGAVATI VISHWAVIDHYALAYA
JABALPUR(M.P)
A PresentationOn
“BLAST”
PresentedBy:
Ambika Prajapati
M. Sc. Biotechnology II Semester

2. BIOINFORMATICS AND SEQUENCE
ALIGNMENT
Bioinformatics involves the analysis of biological information using computers and statistical
techniques,
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein
to identify regions of similarity that may be a consequence of functional, structural, or evolutionary
relationships between the sequences.
The sequence alignment is made between a known sequence and unknown sequence or between two
unknown sequences. The known sequence is called reference sequence. The unknown sequence is called
query sequence .
Types of Alignment :
1. Local Alignment: is a matching of two sequence from regions which have more similarity with each
other..
Input: The two sequences may or may not be related .
Goal: see whether a substring in one sequence aligns well with a substring in the other .
Applications: - Searching for local similarities in large sequences.

3. 2. Global Alignment: matches the identical sequences, it is a matching the residues of
two sequences across their entire length.
Input: treat the two sequences as potentially equivalent .
Goal: identify conserved regions and differences.
Applications: -
Comparing two genes with same function (in human vs mouse).
Comparing two proteins with similar function.
Local Alignment Global Alignment
SEQUENCE ALIGNMENT
BLAST FASTA

4. BLAST - INTRODUCTION
BLAST stands for Basic Local Alignment Search Tool. It addresses a fundamental problem in
bioinformatics research. BLAST tool is used to compare a query sequence with a library or database of
sequences.
In Bioinformatics, is an algorithm and program for comparing primary biological sequence information,
such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences.
BLAST was developed by stochastic model of Samuel Karlin and Stephen Altschul in 1990. They
proposed “a method for estimating similarities between the known DNA sequence of one organism with
that of another”.
A BLAST search enables a researcher to compare a subject protein or nucleotide sequence (called a
query sequence) with a library or database of sequences and identify database sequences that resemble
the query sequence above a certain threshold.

5. BLAST finds regions of similarity between biological sequences. The program compares nucleotide or
protein sequences to sequence databases and calculates the statistical significance of matches. BLAST
can be used to infer functional and evolutionary relationships between sequences as well as help identify
members of gene families.
It was originally developed in 1990 and controlled by NCBI.
For example, following the discovery of a previously unknown gene in the mouse, a scientist will
typically perform a BLAST search of the human genome to see if humans carry a similar gene; BLAST
will identify sequences in the human genome that resemble the mouse gene based on similarity of
sequence.
BLAST is available on the web on the NCBI website. Different types of BLAST are available according
to the query sequences and the target databases. BLAST is more time-efficient than FASTA by searching
only for the more significant patterns in the sequences, yet with comparative sensitivity.

6. VARIANTS OF BLAST
BLASTN - Compares a DNA query to a DNA database. Searches both strands
automatically. It is optimized for speed, rather than sensitivity.
BLASTP - Compares a protein query to a protein database.
BLASTX - Compares a DNA query to a protein database, by translating the
query sequence in the 6 possible frames and comparing each against the
database (3 reading frames from each strand of the DNA) searching.
TBLASTN - Compares a protein query to a DNA database, in the 6 possible
frames of the database.
TBLASTX - Compares the protein encoded in a DNA query to the protein
encoded in a DNA database, in the 6 possible frames of both query and
database sequences.

7. INPUT-OUTPUT
Input
Input sequences (in FASTA or Genbank format), database to search
and other optional parameters such as scoring matrix.
Output
BLAST output can be delivered in a variety of formats. These formats
include HTML, plain text, and XML formatting. For NCBI web-page,
the default format for output is HTML. When performing a BLAST on
NCBI, the results are given in a graphical format showing the hits
found, a table showing sequence identifiers for the hits with scoring
related data, as well as alignments for the sequence of interest and the
hits received with corresponding BLAST scores for these. The easiest
to read and most informative of these is probably the table.

8. BLAST STEPS
• Step 1:- Go to Google and type NCBI and open it.
• Step 2:- In NCBI Homepage , on the extreme right, under the heading- Popular Resources, Click on
the BLAST and open it.
• Step 3:- In BLAST, there are various options available. If you want to align Nucleotides (DNA
Sequence), then open Nucleotide BLAST and if you want to align Proteins, then open Protein
BLAST.
• Step 4 :- In BLAST tab, under Enter Query Sequence - Type Accession Number or FASTA Sequence
there.
• Step 5 :- The next is Choose Search set. In Database, select Standard database. In organism ,write the
name of the organism you want to include or exclude.
• Step 6 :- The last is Program selection – select Highly Similar Sequences (MegaBLAST).
• Step 7 :- Click on the BLAST and compare the entered query sequence with library or database of
sequences and identify database sequences that resemble the query sequence.

10. APPLICATIONS OF BLAST
These include identifying species, locating domains, establishing phylogeny, DNA mapping, and
comparison.
• Identifying species
With the use of BLAST, you can possibly correctly identify a species or find homologous species. This
can be useful, for example, when you are working with a DNA sequence from an unknown species.
• Locating domains
When working with a protein sequence you can input it into BLAST, to locate known domains within
the sequence of interest.
• Establishing phylogeny
Using the results received through BLAST you can create a phylogenetic tree using the BLAST web-
page.

11. • DNA mapping
When working with a known species and looking to sequence a gene at an unknown location, BLAST
can compare the chromosomal position of the sequence of interest, to relevant sequences in the
database(s). NCBI has a "Magic-BLAST" tool built around BLAST for this purpose.
• Comparison
When working with genes, BLAST can locate common genes in two related species, and can be used to
map annotations from one organism to another.

12. REFERENCES
1. https://www.slideshare.net/mobile/Fardin6600/blast-algorithm
2. https://en.m.wikipedia.org/wiki/BLAST_(biotechnology)#:~:text=In%20bioinformatics%2
C%20BLAST%20
3. https://www.limswiki.org/index.php/Bioinformatics
4. https://www.slideshare.net/mobile/arundhatimehta50/blast-63513285
5. https://www.slideshare.net/mobile/queenmalik/blast-71256508
6. https://www.slideshare.net/mobile/ArifulIslamSagar/blast-basic-local-alignment-search-
tool
7. Shomu’s Biology : Youtube Channel
https://www.youtube.com/user/TheFunsuman