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EMBOSS: stamps |
The modified code is kept on the HGMP file system in /packages/stamp/src2 WHEN RUNNING STAMPS AT THE HGMP IT IS ESSENTIAL THAT THE COMMAND 'use stamp2' (which runs the script /packages/menu/USE/stamp2) IS GIVEN BEFORE STAMPS IS RUN. This will ensure that the modified version of stamp is used.
% stamps
Mandatory qualifiers: [-scopf] infile Name of scop file for input (embl-like format) [-path] string Location of alignment files for output Optional qualifiers: (none) Advanced qualifiers: (none) General qualifiers: -help bool report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-scopf] (Parameter 1) |
Name of scop file for input (embl-like format) | Input file | Escop.dat |
[-path] (Parameter 2) |
Location of alignment files for output | Any string is accepted | ./ |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
(none) |
The format of the stamps output file (Figure 1) is similar to the output file generated by stamp when issued with the following three types of command:
(1) stamp -l ./stamps_file.dom -s -n 2 -slide 5 -prefix ./stamps_file -d ./stamps_file.set;sorttrans -f ./stamps_file.scan -s Sc 2.5 > ./stamps_file.sort;stamp -l ./stamps_file.sort -prefix ./stamps_file > ./stamps_file.log
(2) poststamp -f ./stamps_file.3 -min 0.5
(3) ver2hor -f ./stamps_file.3.post > ./stamps_file.out
However, the SCOP classification records for the appopriate family are written above the alignment, no dssp assignments are given, and only the 'Post similar' line is given. Also, 7 character domain identifier codes taken from the scop classificaiton file are given.
Figure 1 Example of stamps output file CL All alpha proteins XX FO Globin-like XX SF Globin-like XX FA Globins XX Number 10 20 30 40 50 d1vrea_ LSAAQRQVVASTWKDIAgsdngAGVGKECFTKFLSAHHDMAAV f gFS d3sdhb_ svydaaaqLTADVKKDLRDSWKVIG sd kKGNGVALMTTLFADNQETIGYfkrlGN d3hbia_ svydaaaqLTADVKKDLRDSWKVIG sd kKGNGVALMTTLFADNQETIGYfkrlGN d3sdha_ svydaaaqLTADVKKDLRDSWKVIG sd kKGNGVALMTTLFADNQETIGYfkrlGN Post_similar --------11111111111111111-00-1111111111111111111111-0-111 Number 60 70 80 90 100 110 d1vrea_ GAS dpGVADLGAKVLAQIGVAVSHLgDEGKMVAEMKAVGVRHKgygnkhIKAEY d3sdhb_ VSQgmandKLRGHSITLMYALQNFIDQLdNPDDLVCVVEKFAVNHI t rkISAAE d3hbia_ VSQgmandKLRGHSITLMYALQNFIDQLdNPDDLVCVVEKLAVNHI t rkISAAE d3sdha_ VSQgmandKLRGHSITLMYALQNFIDQLdNPDDLVCVVEKFAVNHI t rkISAAE Post_similar 111---0011111111111111111111011111111111111111--0-0011111 Number 120 130 140 150 160 d1vrea_ FEPlGASL LSAMEhriggkMNAAAKDAWAAAYADisgalisglqs d3sdhb_ FGK INGPiKKVLA s k nFGDKYANAWAKLVAVvqa al d3hbia_ FGK INGPiKKVLA s k nFGDKYANAWAKLVAVvqa al d3sdha_ FGK INGPiKKVLA s k nFGDKYANAWAKLVAVvqa al Post_similar 111-1111-11111-0-0-1111111111111111100-00-----
Program name | Description |
---|---|
scopalign | Generate alignments for SCOP families |