help:matrix [2008/07/02 09:54]
127.0.0.1 external edit |
help:matrix [2012/11/30 15:22] (current)
|
| | ====== About Matrices ====== | | ====== About Matrices ====== |
| | | | |
| | + | For more information see [[http://www.ebi.ac.uk/help/matrix.html|Matrix Help Page]]. |
| | | | |
| - | ^ Tool ^ Matrices supported ^ | + | ===== Protein Matrices ===== |
| - | | FASTA | BLOSUM50 BLOSUM62 BLOSUM80 PAM120 PAM250 MDM10 MDM20 MDM40 | | + | |
| - | | NCBI BLAST | BLOSUM45 BLOSUM45 BLOSUM62 BLOSUM80 PAM30 PAM70 | | + | |
| - | | ScanPS | blosum35 blosum50 blosum62 pam30 pam100 pam250 | | + | |
| - | | WU-BLAST | BLOSUM30 BLOSUM35 BLOSUM40 BLOSUM45 BLOSUM50 BLOSUM62 BLOSUM65 BLOSUM70 BLOSUM75 BLOSUM80 BLOSUM85 BLOSUM90 BLOSUM100 GONNET PAM10 PAM20 PAM30 PAM40 PAM50 PAM60 PAM70 PAM80 PAM90 PAM100 PAM110 PAM120 PAM130 PAM140 PAM150 PAM160 PAM170 PAM180 PAM190 PAM200 PAM210 PAM220 PAM230 PAM240 PAM250 PAM260 PAM270 PAM280 PAM290 PAM300 PAM310 PAM320 PAM330 PAM340 PAM350 PAM360 PAM370 AM380 PAM390 PAM400 PAM410 PAM420 PAM430 PAM440 PAM450 PAM460 PAM470 PAM480 PAM490 PAM500 | | + | |
| | | | |
| - | For more information see [[http://www.ebi.ac.uk/help/matrix.html | Matrix Help Page]] | + | ^ Tool ^ Matrix ^ Option Value ^ |
| | + | | EMBOSS | BLOSUM30 | EBLOSUM30 | |
| | + | | | BLOSUM35 | EBLOSUM35 | |
| | + | | | BLOSUM40 | EBLOSUM40 | |
| | + | | | BLOSUM45 | EBLOSUM45 | |
| | + | | | BLOSUM50 | EBLOSUM50 | |
| | + | | | BLOSUM55 | EBLOSUM55 | |
| | + | | | BLOSUM60 | EBLOSUM60 | |
| | + | | | BLOSUM62 | **EBLOSUM62** | |
| | + | | | BLOSUM62-12 | EBLOSUM62-12 | |
| | + | | | BLOSUM65 | EBLOSUM65 | |
| | + | | | BLOSUM70 | EBLOSUM70 | |
| | + | | | BLOSUM75 | EBLOSUM75 | |
| | + | | | BLOSUM80 | EBLOSUM80 | |
| | + | | | BLOSUM85 | EBLOSUM85 | |
| | + | | | BLOSUM90 | EBLOSUM90 | |
| | + | | | BLOSUMN | EBLOSUMN | |
| | + | | | PAM10 | EPAM10 | |
| | + | | | PAM20 | EPAM20 | |
| | + | | | PAM30 | EPAM30 | |
| | + | | | PAM40 | EPAM40 | |
| | + | | | PAM50 | EPAM50 | |
| | + | | | PAM60 | EPAM60 | |
| | + | | | PAM70 | EPAM70 | |
| | + | | | PAM80 | EPAM80 | |
| | + | | | PAM90 | EPAM90 | |
| | + | | | PAM100 | EPAM100 | |
| | + | | | PAM110 | EPAM110 | |
| | + | | | PAM120 | EPAM120 | |
| | + | | | PAM130 | EPAM130 | |
| | + | | | PAM140 | EPAM140 | |
| | + | | | PAM150 | EPAM150 | |
| | + | | | PAM160 | EPAM160 | |
| | + | | | PAM170 | EPAM170 | |
| | + | | | PAM180 | EPAM180 | |
| | + | | | PAM190 | EPAM190 | |
| | + | | | PAM200 | EPAM200 | |
| | + | | | PAM210 | EPAM210 | |
| | + | | | PAM220 | EPAM220 | |
| | + | | | PAM230 | EPAM230 | |
| | + | | | PAM240 | EPAM240 | |
| | + | | | PAM250 | EPAM250 | |
| | + | | | PAM260 | EPAM260 | |
| | + | | | PAM270 | EPAM270 | |
| | + | | | PAM280 | EPAM280 | |
| | + | | | PAM290 | EPAM290 | |
| | + | | | PAM300 | EPAM300 | |
| | + | | | PAM310 | EPAM310 | |
| | + | | | PAM320 | EPAM320 | |
| | + | | | PAM330 | EPAM330 | |
| | + | | | PAM340 | EPAM340 | |
| | + | | | PAM350 | EPAM350 | |
| | + | | | PAM360 | EPAM360 | |
| | + | | | PAM370 | EPAM370 | |
| | + | | | PAM380 | EPAM380 | |
| | + | | | PAM390 | EPAM390 | |
| | + | | | PAM400 | EPAM400 | |
| | + | | | PAM410 | EPAM410 | |
| | + | | | PAM420 | EPAM420 | |
| | + | | | PAM430 | EPAM430 | |
| | + | | | PAM440 | EPAM440 | |
| | + | | | PAM450 | EPAM450 | |
| | + | | | PAM460 | EPAM460 | |
| | + | | | PAM470 | EPAM470 | |
| | + | | | PAM480 | EPAM480 | |
| | + | | | PAM490 | EPAM490 | |
| | + | | | PAM500 | EPAM500 | |
| | + | | FASTA | BLOSUM50 | **BL50** | |
| | + | | | BLOSUM62 | BL62 | |
| | + | | | BLOSUM80 | BL80 | |
| | + | | | MDM10 | M10 | |
| | + | | | MDM20 | M20 | |
| | + | | | MDM40 | M40 | |
| | + | | | PAM120 | P120 | |
| | + | | | PAM250 | P250 | |
| | + | | NCBI BLAST | BLOSUM45 | blosum45 | |
| | + | | | BLOSUM50 | blosum50 | |
| | + | | | BLOSUM62 | **blosum62** | |
| | + | | | BLOSUM80 | blosum80 | |
| | + | | | BLOSUM90 | blosum90 | |
| | + | | | PAM30 | pam30 | |
| | + | | | PAM70 | pam70 | |
| | + | | | PAM250 | pam250 | |
| | + | | WU-BLAST | BLOSUM30 | blosum30 | |
| | + | | | BLOSUM35 | blosum35 | |
| | + | | | BLOSUM40 | blosum40 | |
| | + | | | BLOSUM45 | blosum45 | |
| | + | | | BLOSUM50 | blosum50 | |
| | + | | | BLOSUM62 | **blosum62** | |
| | + | | | BLOSUM65 | blosum65 | |
| | + | | | BLOSUM70 | blosum70 | |
| | + | | | BLOSUM75 | blosum75 | |
| | + | | | BLOSUM80 | blosum80 | |
| | + | | | BLOSUM85 | blosum85 | |
| | + | | | BLOSUM90 | blosum90 | |
| | + | | | BLOSUM100 | blosum100 | |
| | + | | | GONNET | GONNET | |
| | + | | | PAM10 | pam10 | |
| | + | | | PAM20 | pam20 | |
| | + | | | PAM30 | pam30 | |
| | + | | | PAM40 | pam40 | |
| | + | | | PAM50 | pam50 | |
| | + | | | PAM60 | pam60 | |
| | + | | | PAM70 | pam70 | |
| | + | | | PAM80 | pam80 | |
| | + | | | PAM90 | pam90 | |
| | + | | | PAM100 | pam100 | |
| | + | | | PAM110 | pam110 | |
| | + | | | PAM120 | pam120 | |
| | + | | | PAM130 | pam130 | |
| | + | | | PAM140 | pam140 | |
| | + | | | PAM150 | pam150 | |
| | + | | | PAM160 | pam160 | |
| | + | | | PAM170 | pam170 | |
| | + | | | PAM180 | pam180 | |
| | + | | | PAM190 | pam190 | |
| | + | | | PAM200 | pam200 | |
| | + | | | PAM210 | pam210 | |
| | + | | | PAM220 | pam220 | |
| | + | | | PAM230 | pam230 | |
| | + | | | PAM240 | pam240 | |
| | + | | | PAM250 | pam250 | |
| | + | | | PAM260 | pam260 | |
| | + | | | PAM270 | pam270 | |
| | + | | | PAM280 | pam280 | |
| | + | | | PAM290 | pam290 | |
| | + | | | PAM300 | pam300 | |
| | + | | | PAM310 | pam310 | |
| | + | | | PAM320 | pam320 | |
| | + | | | PAM330 | pam330 | |
| | + | | | PAM340 | pam340 | |
| | + | | | PAM350 | pam350 | |
| | + | | | PAM360 | pam360 | |
| | + | | | PAM370 | pam370 | |
| | + | | | PAM380 | pam380 | |
| | + | | | PAM390 | pam390 | |
| | + | | | PAM400 | pam400 | |
| | + | | | PAM410 | pam410 | |
| | + | | | PAM420 | pam420 | |
| | + | | | PAM430 | pam430 | |
| | + | | | PAM440 | pam440 | |
| | + | | | PAM450 | pam450 | |
| | + | | | PAM460 | pam460 | |
| | + | | | PAM470 | pam470 | |
| | + | | | PAM480 | pam480 | |
| | + | | | PAM490 | pam490 | |
| | + | | | PAM500 | pam500 | |
| | + | |
| | + | ===== Nucleotide Matrices ===== |
| | + | |
| | + | ^ Tool ^ Matrix ^ Option Value ^ |
| | + | | EMBOSS | DNA, with ambiguity | **EDNAFULL** | |
| | + | | | DNA, identity only | EDNAMAT | |
| | + | | FASTA | //none// | | |
| | + | | NCBI BLAST | //match/missmatch scores used// | | |
| | + | | WU-BLAST | Identity 4.2 | identity.4.2 | |
| | + | | | Identity 4.4 | identity.4.4 | |
| | | | |
