BLAST

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 Presentation On “BLAST” Presented By: Ambika Prajapati M. Sc. Biotechnology II Semester This Photo by Unknown Author is licensed under CC BY-NC

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 sequenc e . Types o f 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  B ioinformatics , 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.

9. 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.

10. 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.

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