There are two ways to display STAMP alignments in a vertical format.
The first is simply to use ACONVERT to change the STAMP block file format into
another such as MSF or CLUSTAL. The format would be:
aconvert -in b -out c < <stamp alignment file>
Where `-out c' denotes CLUSTAL format (using `-out m' would give MSF format).
ACONVERT does not use any of the STAMP specific parts of the alignment (i.e reliable
structural equivalences, etc.). There is a program specifically designed for displaying
these data in a vertical format. VER2HOR takes a STAMP alignment file and outputs a
horizonal text format. For example, to display the globin alignment, one needs to
type:
ver2hor -f globin.5.clean
to give (see examples/globin/globin.5.ver2hor):
VER2HOR R.B. Russell, 1995
Prints STAMP alignments in horizontal format
for quick viewing
Reading Alignment...
Blocfile read: Length: 163
Getting STAMP information...
6 STAMP fields read in for 163 positions
Processing the alignment...
Output:
Very reliable => Pij' >=6 for stretches of >=3
Less reliable => Pij' >=4.5 for stretches of >=3
Post reliable => All Pij' > stamp_post parameter for stretches >=3
Number 10 20 30 40 50
1lh1 gaLTESQAALVKSSWEEfnanipKHTHRFFILVLEIAPAAKDLFSFLkg
2lhb pivdtgsvapLSAAEKTKIRSAWAPvystyeTSGVDILVKFFTSTPAAQEFFPKFkg
1ecd LSADQISTVQASFDKv kGDPVGILYAVFKADPSIMAKFTQFag
4mbn vLSEGEWQLVLHVWAKveadvaGHGQDILIRLFKSHPETLEKFDRFkh
2hhbb vhLTPEEKSAVTALWGKvn vdEVGGEALGRLLVVYPWTQRFFESFgd
2hhba vLSPADKTNVKAAWGKvgahagEYGAEALERMFLSFPTTKTYFPHF
1lh1_dssp ----HHHHHHHHHHHHHhhtthhHHHHHHHHHHHHH-GGGGGG-TTTtt
2lhb_dssp ---sss------HHHHHHHHHHHHHhhhthhHHHHHHHHHHHHH-GGGGGG-GGGtt
1ecd_dssp --HHHHHHHHHHHHTt tT-HHHHHHHHHHH-HHHHTT-TTTtt
4mbn_dssp --HHHHHHHHHHHHHGg--hhhHHHHHHHHHHHHHHHHHGGGG----s
2hhbb_dssp ----HHHHHHHHHHHTT-- hhHHHHHHHHHHHHHSGGGGGG-GGG--
2hhba_dssp ---HHHHHHHHHHHHHhggghhHHHHHHHHHHHHH-GGGGGG-TTS
Very similar ----------1111111111111110----0111111111111111111111111--
Less similar ----------1111111111111110----0111111111111111111111111--
Post similar ----------1111111111111110----0111111111111111111111111--
<etc.>
The sequences are displayed, as are the DSSP secondary structures and three measures of similarity (explained at the top of the output). One can suppress the displaying of secondary structures by the option `-sec false', or can display a summary of the secondary structures (an average) by typing `-secsum true'. Try these and see. The column width can be modified by using `-columns <value>'. The remaning parameters are as for DSTAMP (see next section).