BLAST
M. HUZAIFA ARSHAD
ROLL NO. 16024
 Sequence Alignment
 Introduction to BLAST
 Background
 Algorithm
CONTENTS
 Steps
 Variants
 How to perform BLAST
 Results of BLAST
 Work cited
 A process for comparing biological sequences
SEQUENCE
ALIGNMENT
 Pairwise sequence alignment vs Multiple sequence
alignment
 Local alignment and Global alignment
 Gap Penalties
CONT.
Gaps
 BASIC LOCAL ALIGNMENT SEARCH TOOL
(BLAST) [https://blast.ncbi.nlm.nih.gov/Blast.cgi]
INTRODUCTION
TO BLAST
 Developed by Stephen Altschul of NCBI in 1990
 Uses heuristics to align a query sequence with all
sequences in a database
 BLAST algorithm is tuned to find the domains of
Proteins
 3 unique requirements for implementing algorithms
BACKGROUND
 Sensitivity
 Selectivity / Specificity
 Speed
 Dynamic programming methods; too slow and
impractical when computational resources are limited
CONT.
 To speed up the comparison, heuristic methods must be used
 No guarantee of finding the optimal alignment or true homologs
 50–100 times faster than dynamic programming
 Use of heuristic “word” method for fast pairwise
sequence alignment
ALGORITHM
 Works by finding short stretches of identical or
nearly identical letters in two sequences
 Short strings of characters are called “words”
CONT.
 Basic assumption; Two related sequences must have at least one word in
common
 First identifying word matches, a longer alignment can be obtained by
extending similarity regions from the words
 Create a list of words from the query sequence
STEPS
 Search a sequence database for the occurrence of
these words
 Pairwise alignment by extending from the words in
both directions
 Extension continues until the score of the alignment
drops below a threshold due to mismatches
CONT.
 Drop threshold is 22 for proteins and 20 for DNA
 High-scoring segment pair (HSP)
CONT.
EXAMPLE
BLAST is a family of programs that includes:
 megaBLAST
VARIANTS
 BLASTN
 BLASTP
 BLASTX
 TBLASTN
CONT.
 TBLASTX
 PSI-BLAST
 RPSBLAST
 DELTA-BLAST
HOW TO PERFORM BLAST?
PASTE SEQUENCE IN FASTA FORMAT
CHOOSE DATABASE
CHOOSE ALGORITHM
RESULTS OF
BLAST
 Graphical view
 Hits
 Alignment
GRAPHICAL SUMMARY
HITS
ALIGNMENTS
• https://www.ncbi.nlm.nih.gov/books/NBK153387/
WORKS CITED
• Xiong, Jin. Essential
University Press, 2006.
bioinformatics.
Cambridge