Bioinformatics

1. POOJA SEVAK
MSC II
PAPER III
BLAST
( Basic Local Alignment Search Tool)

2. Introduction
 BLAST is a sequence similarity search program that
can be used to quickly search a sequence database
for matches to a query sequence.
 Set of programs that search sequence databases for
statistically significant similarities.

3.  Basic Local Alignment Search Tool
– Altschul et al. 1990,1994,1997
 Heuristic method for local alignment
 Designed specifically for database searches
 Based on the same assumption as FASTA that good
alignments contain short lengths of exact matches

4.  Both BLAST and FASTA search for local sequence
similarity ‐ indeed they have exactly the same goals,
though they use somewhat different algorithms and
statistical approaches.
 BLAST benefits
– Speed
– User friendly
– Statistical rigor
– More sensitive

5. Input/Output
 Input:
– Query sequence Q
– Database of sequences DB
– Maximal E‐value
 Output:
– Sequences from DB (Seq), such that Q and Seq
have E‐values < E

6. Type Of BLAST

7.  Uses word matching like FASTA
 Similarity matching of words (3 amino acids, 11
bases)
– does not require identical words.
 If no words are similar, then no alignment
– Will not find matches for very short sequences
 Does not handle gaps well
 “gapped BLAST” is somewhat better

8. BLAST Algorithm
3 step process
1. Word search method
2. Identification of exact word match method
3. Maximum segment pair alignment method

9. BLAST Algorithm

10. BLAST word matching

11. Find Location Of Matching Words In
Dataabase Sequences

12. Extend Hits One Position At A Time

13.  Use two word matches as anchors to build an
alignment between the query and a database
sequence.
 Then score the alignment.

14. HSPs are Aligned Regions
 The results of the word matching and attempts to
extend the alignment are segments‐ called HSPs
(High‐Scoring Segment Pairs)
 BLAST often produces several short HSPs
rather than a single aligned region

15. REFERENCEs
 Bioinformatics by Attwood
 http://www.youtube.com/watch?v=LlnMtI2Sg4g