Difference between revisions of "BLAST/matrices"
From Christoph's Personal Wiki
| (One intermediate revision by the same user not shown) | |||
| Line 1: | Line 1: | ||
The following are the standard '''[[BLAST]] matrices''' provided by NCBI (last access date: 2008-05-15): | The following are the standard '''[[BLAST]] matrices''' provided by NCBI (last access date: 2008-05-15): | ||
| + | |||
| + | see: [[wikipedia:Substitution matrix|Substitution matrix]] | ||
==BLOSUM== | ==BLOSUM== | ||
| + | '''[[wikipedia:BLOSUM|BLOSUM]]''' ('''BLO'''cks of amino acid '''SU'''bstitution '''M'''atrix) | ||
| + | |||
*[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM100] | *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM100] | ||
*[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM100.50] | *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUM100.50] | ||
| Line 34: | Line 38: | ||
*[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUMN] | *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUMN] | ||
*[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUMN.50] | *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ BLOSUMN.50] | ||
| + | |||
==PAM== | ==PAM== | ||
| + | '''[[wikipedia:Point Accepted Mutation|PAM]]''' ('''P'''oint '''A'''ccepted '''M'''utation) | ||
| + | |||
*[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM10] | *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM10] | ||
*[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM100] | *[ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ PAM100] | ||
Latest revision as of 01:07, 16 May 2008
The following are the standard BLAST matrices provided by NCBI (last access date: 2008-05-15):
see: Substitution matrix
Contents
BLOSUM
BLOSUM (BLOcks of amino acid SUbstitution Matrix)
- BLOSUM100
- BLOSUM100.50
- BLOSUM30
- BLOSUM30.50
- BLOSUM35
- BLOSUM35.50
- BLOSUM40
- BLOSUM40.50
- BLOSUM45
- BLOSUM45.50
- BLOSUM50
- BLOSUM50.50
- BLOSUM55
- BLOSUM55.50
- BLOSUM60
- BLOSUM60.50
- BLOSUM62
- BLOSUM62.50
- BLOSUM65
- BLOSUM65.50
- BLOSUM70
- BLOSUM70.50
- BLOSUM75
- BLOSUM75.50
- BLOSUM80
- BLOSUM80.50
- BLOSUM85
- BLOSUM85.50
- BLOSUM90
- BLOSUM90.50
- BLOSUMN
- BLOSUMN.50
PAM
PAM (Point Accepted Mutation)
- PAM10
- PAM100
- PAM110
- PAM120
- PAM120.cdi
- PAM130
- PAM140
- PAM150
- PAM160
- PAM160.cdi
- PAM170
- PAM180
- PAM190
- PAM20
- PAM200
- PAM200.cdi
- PAM210
- PAM220
- PAM230
- PAM240
- PAM250
- PAM250.cdi
- PAM260
- PAM270
- PAM280
- PAM290
- PAM30
- PAM300
- PAM310
- PAM320
- PAM330
- PAM340
- PAM350
- PAM360
- PAM370
- PAM380
- PAM390
- PAM40
- PAM40.cdi
- PAM400
- PAM410
- PAM420
- PAM430
- PAM440
- PAM450
- PAM460
- PAM470
- PAM480
- PAM490
- PAM50
- PAM500
- PAM60
- PAM70
- PAM80
- PAM80.cdi
- PAM90
Other
- DAYHOFF
- GONNET
- IDENTITY
- MATCH
- NUC.4.2 — Uses ambiguous nucleotide codes, probabilities rounded to nearest integer
- NUC.4.4 — Uses ambiguous nucleotide codes, probabilities rounded to nearest integer
