Blast

It includes the information related to a bioinformatics tool BLAST (Basic Local Alignment Search Tool), BLAST is in-silico hybridisation to find regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. This presentation too contains the input - output format, Blast process and its types .

1. PRESENTED BY : Arundhati mehta b.s c. Biotechnology Vi semester 13202008 BLAST ( A Bioinformatics tool ) © Arundhati Mehta 2016

2. BIOINFORMATICS It is the science of managing and analyzing biological data ( informations associated with biomolecules like DNA, RNA, Protein etc.) using advanced computing techniques. Software tools for bioinformatics range from simple command-line tools , to more complex graphical programs and stand alone web-services available from various bioinformatics companies or public institutions.

3. Introduction to BLAST It is a sequence similarity search program for comparing biological sequences such as amino acid sequence of different proteins or the nucleotides of DNA sequences with sequence database or library sequences. It is an Insilico Hybridisation experiment used to identify significant similarities between query sequences with the library sequences. BLAST stands for : B - Basic L - Local A - Alignment S - Search T - Tool

4. BLAST was designed by Eugene Myers , Samuel Karlin , Stephen Altschul , Warren Gish, David J. Lipman and Webb Miller ( 1990,1994,1997 ) at the National Institute of Health and was published in Journal of Molecular Biology in 1990. It was originally developed & controlled by NCBI . Link: http://www.ncbi.nlm.nih.gov/BLAST/

5. NCBI Home Page

6. NCBI- BLAST Home Page

7. EMBL-EBI Home Page

8. EMBL-EBI BLAST Page

9. BLAST - Input & Output Default database is the non-redundant (nr) database maintained by NCBI. All BLAST programs use a substitution scoring matrix (BLOSUM or PAM), determines pair-wise raw alignment scores.

10. BLAST PROCESS BLAST works through use of Heuristic Algorithm , an algorithm that is able to produce an acceptable solution to a problem in many practical scenarios and is more faster than classical methods. Heuristics are typically used when there is no known method to find an optimal solution ,under the given constraints . Using this BLAST finds homologous sequences , not by comparing either sequences in its entirety, but rather by locating short matches between the two sequences. While attempting to find the homology sequences , sets of common letters are known as WORDS.

11. BLAST Types Blastp : compares protein query against proteins sequence database. tBlastn : compares protein query against the all six reading frames of a translated nucleotide sequence database. Blastn : compares nucleotide query against nucleotide sequence database. Blastx : compares six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database. tBlastx : compares nucleotide query against translated nucleotide sequence database.

12. BLAST Search

13. BLAST Search

14. Graphic summary Query sequence is at the top, with colour key for alignment scores. Each bar represents the portion of another sequence that’s similar to your query sequence :- Red bars- most similar sequence Pink bars- match less good Green bars- not impressive match Blue bars- worst score Black bars- Bad hits

15. 1 - This portion of each description links to the sequence record for a particular hit. 2 - Score or bit score is a value calculated from the number of gaps and substitutions associated with each aligned sequence. The higher the score, the more significant the alignment. Each score links to the corresponding pairwise alignment between query sequence and hit sequence (also referred to as subject sequence). 3 - E Value (Expect Value) describes the likelihood that a sequence with a similar score will occur in the database by chance . The smaller the E Value, the more significant the alignment 4 - These links provide the user with direct access from BLAST results to related entries in other databases. ‘ L ’ links to Locus Link records and ‘ S ’ links to structure records in NCBI's Molecular Modelling DataBase .

16. The Percentage of identity: This gives you a concrete substitute for the E-value . An identity of more than 25 percent is good news . ( The identity is the number of identical residues divided by the number of matched residues — gaps are simply ignored .) The Positives field gives you a measure of the fraction of residues that are either identical or similar — represented with a + on the actual alignment. The Gaps field shows residues that were not aligned . Length : is alignment length of sequence aligned by BLAST. Top sequence : Query sequence Bottom sequence : Hits ( referred as Subject sequence ) line between sequences : + sign (similar amino acids) space (mismatch) letter (identical residues) XXXX Region : low- complexity segments Numbers : to the right side indicate the coordinates of the match on query & on Hit sequence.

17. BLAST Statistics R = aI + bX - cO - dG Percentage of Identities % I = No. of identical residues -------------------------------- x 100 No. of matched residues Raw scores

18. Applications of BLAST BLAST can be used for several purposes. These include: Identifying Species: With the use of BLAST, you can possibly correctly identify a species and/or find homologous species. This can be useful, for example, when one is working with a DNA sequence from an unknown species. Establishing Phylogeny: Using the results received through BLAST, one can create a phylogenetic tree using the BLAST web-page.

19. Applications of BLAST 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). Locating Domains: When working with a protein sequence you can input it into BLAST, to locate known domains within the sequence of interest. 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.

20. QUESTIONS ???