There are two ways to display STAMP alignments in a horizontal format.
The first is simply to use ACONVERT to change the STAMP block file format into
another format such as MSF or Clustal. The format would be:
aconvert -in b -out c < <stamp alignment file>
Where `-out c' denotes Clustal 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).
the display of secondary structures can be suppressed using the option `-sec false';
a summary of the secondary structures (an average) can be displayed by using the `-secsum true' option.
The column width can be modified by using `-columns 
value
'. The
remaning parameters are as for DSTAMP (see next section).