BLAST (Basic Local Alignment Search Tool)
BLAST (Basic Local Alignment Search Tool)
or
G 0 0 3 6
C 0 1 4 3
T 0 2 1, 0
A 0 0 0 0
- 0 0 0 0
0 - T C G
Match +2, mismatch 0, gap -1
ATCG
T –GC
AT- CG
TGC
G 0 0 3 2
C 0 1 2 3
T 0 2 1 0
A 0 0 0 0
- 0 0 0 0
0 - T G C
A-GCT A-CGT
Smith- AGC-T ACGT
AGCT
Watermann
T 0 0 2 3 4
algorithm
G 0 0 3 2 3
C 0 1 2 3 2
A 0 2 1 0 0
- 0 0 0 0 0
0 - A G C T
Indels
X-A-T-G-C-C-A-C-X X-A-T-G-C-C-A-C-X X-A-T-G-C-C-A-C-X
X-A-T-G-C-C-A-C-X X-A-T-C-C-A-C-X X-A-T-_-C-C-A-C-X
Gap inserted to achieve
identical deleted G optimal (identical)
alignment
BLAST2 DNA or DNA or Comparison between two sequences Find level of seq
protein protein similarity or
identity between
the input seq
BLAST DNA DNA Compares NA query seq against NA Find DNA seq
N database that match the
query
BLAST P Protein Protein Compares protein query seq against Find identical or
protein database homologous
proteins
BLAST DNA Protein Compares Translated NA seq against a Find what
X protein sequence database protein the query
seq codes for
T BLAST Protein DNA Compares aa query seq against Find genes in
N translation of all possible reading unknown DNA
frames of seqs in NA database sequence
Pairwise Alignment Multiple sequence alignment
STA
NEQK
NHQK
NDEQ
QHRK
MILV
MILF
HY
FYW
• A . (period) indicates conservation between groups of weakly similar
properties as below - roughly equivalent to scoring =< 0.5 and > 0 in the
Gonnet PAM 250 matrix:
CSA
ATV
SAG
STNK
STPA
SGND
SNDEQK
NDEQHK
NEQHRK
FVLIM
HFY
• ATGCAT
• ATCG-AT match +1 mismatch -2 gap 0
• +1+1-2-2+1+1=0
• +1+1+0+1+0+1+1=5
• AT-GCAT
• ATCG-AT
• indels