BLAST: Basic Local Analysis

Search Tool

David Requena Anicama

Laboratorio de Bioinformtica y Biologa molecular UPCH
Laboratorio de Bioinformtica FARVET
david.requena.a@upch.pe

BLAST
Atschul et al.

Alignment heuristic method

Hosted by NCBI
Downloadable

Steps:
Filter LCR or SR: N(nt), X(aa).
High scores
SEG, DUST
XNU

K-letter words:
11(nt) or 3(aa).

Confusion

Steps:
Possible matching words:
A B C
20 20 20

ABC
15

PQG
PEG
PQA

203 possible match

scores

Neighborhood word score (>T)

If T = 13:
12

PQG
PEG
PQA

Steps:
Organizing the selected words:
Searching tree

Extend matches to HSP:

Query
Database

R P P Q G L F
D P P E G V V
-2 7 7 2 6 1 -1
HSP

Steps:
HSP extension:

Keep HSP > S:

Random sequences

Steps:
HSP statistical significance:
SW follows EVD (Gumbel Extreme Value Distribution)
= 1

()

log( )
=

y k Statistical parameters:
Susbtitution matrix
Penalties
Sequence composition

ln

ln

m = Query effective sequence

n = Database effective sequence
H = Expected score of aleatory alignment

E-value:
Nmero de veces que una secuencia de la base de
datos no relacionada puede obtener un score (s)
mayor a x por azar.
= 1

>

D = Number of database sequences.