BLAST Local pairwise alignment heuristic Faster than standard pairwise alignment programs such as SSEARCH but less sensitive Online server httpwwwncbinlmnihgovblast BLAST Given a query ID: 912749
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Slide1
BLAST
BNFO 236
Usman Roshan
Slide2BLAST
Local pairwise alignment heuristic
Faster than standard pairwise alignment programs such as SSEARCH, but less sensitive.
Online server:
http://www.ncbi.nlm.nih.gov/blast
Slide3BLAST
Given a query
q
and a target sequence, find substrings of length
k
(
k
-mers) of score at least
t
--- also called
hits
.
k
is normally 3 to 5 for amino acids and 12 for nucleotides.
Extend each hit to a
locally maximal segment
. Terminate the extension when the reduction in score exceeds a pre-defined threshold
Report maximal segments above score
S
.
Slide4Finding k-mers quickly
Preprocess the database of sequences:
For each sequence in the database store all k-mers in hash-table.
This takes linear time
Query sequence:
For each k-mer in the query sequence look up the hash table of the target to see if it exists
Also takes linear time