DOMAINALIGN documentation


 


CONTENTS

1.0 SUMMARY
2.0 INPUTS & OUTPUTS
3.0 INPUT FILE FORMAT
4.0 OUTPUT FILE FORMAT
5.0 DATA FILES
6.0 USAGE
7.0 KNOWN BUGS & WARNINGS
8.0 NOTES
9.0 DESCRIPTION
10.0 ALGORITHM
11.0 RELATED APPLICATIONS
12.0 DIAGNOSTIC ERROR MESSAGES
13.0 AUTHORS
14.0 REFERENCES



1.0 SUMMARY

Generate alignments (DAF file) for nodes in a DCF file


2.0 INPUTS & OUTPUTS

DOMAINALIGN generates a DAF file (domain alignment file) for each user-defined node (e.g. family or superfamily) in a DCF file (domain classification file) that is read. Each DAF file contains a structure-based sequence alignment annotated with domain classification data. If the STAMP algorithm is used, structural superimpositions are also generated and saved to file (PDB format). The alignments are calculated by using STAMP or TCOFFEE and these applications must be installed on the system that is running DOMAINALIGN (see 'Notes' below).
Clearly no alignment can be generated for nodes with a single entry (domain) only: sequences for such domains are (optionally) written to file (fasta format).
DOMAINALIGN requires a directory of domain PDB files; the path and extension of these must be set by the user (via the ACD file) and also specified in the STAMP "pdb.directories" file (see 'Notes' below)
A log file of diagnostic messages is written. The identifier (e.g SCOP Sunid) of the nodes from the DCF file are used to name the output files. The user also specifies the input file, paths for the two types of alignment files (output), path of singlet sequence files (if output) and name of log file.


3.0 INPUT FILE FORMAT

The format of the DCF (domain classification file) is described in SCOPPARSE documentation

Input files for usage example

File: all.scop2

ID   D1CS4A_
XX
EN   1CS4
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 55073 SF; 55074 FA; 55077 DO; 55078 SO; 39418 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Adenylyl and guanylyl cyclase catalytic domain
XX
FA   Adenylyl and guanylyl cyclase catalytic domain
XX
DO   Adenylyl cyclase VC1, domain C1a
XX
OS   Dog (Canis familiaris)
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//
ID   D1FX2A_
XX
EN   1FX2
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 55073 SF; 55074 FA; 55081 DO; 55082 SO; 39430 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Adenylyl and guanylyl cyclase catalytic domain
XX
FA   Adenylyl and guanylyl cyclase catalytic domain
XX
DO   Receptor-type monomeric adenylyl cyclase
XX
OS   Trypanosome (Trypanosoma brucei), different isoform
XX
NC   1
XX
CN   [1]
XX


  [Part of this file has been deleted for brevity]

XX
EN   4AT1
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39019 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
DO   Aspartate carbamoyltransferase
XX
OS   Escherichia coli
XX
NC   1
XX
CN   [1]
XX
CH   B CHAIN; 8 START; 100 END;
//
ID   D4AT1D1
XX
EN   4AT1
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39020 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
DO   Aspartate carbamoyltransferase
XX
OS   Escherichia coli
XX
NC   1
XX
CN   [1]
XX
CH   D CHAIN; 8 START; 100 END;
//




4.0 OUTPUT FILE FORMAT

Structure-based sequence alignment
The DAF (domain alignment file) format (Figure 1) consists of an alignment in EMBOSS "simple" multiple sequence alignment format with domain classification records. All lines other than sequence lines begin with '#' to denote a comment. The domain classification records for the appopriate node from the DCF file are given at the top of the file above the alignment. The records shown are TY (domain type, either SCOP or CATH), CL (class), FO (fold), SF (superfamily) and FA (family). For CATH domains, AR (architecture) and TP (topology) may also be given. Regardless of which node (family, superfamily etc) is represented, a unique identifier for the node is given after SI. Below the classification records, there are blocks that contain the sequence names, positions and aligned sequences. The names are the 7 character domain identifier codes taken from the DCF file. The positions are the start and end residue positions of the appropriate section of sequence. The sequence uses '-' as a gap character. The STAMP 'Post similar' line is given as a markup line underneath the sequence but no dssp assignments are written.

Output files for usage example

File: 54894.ent

REMARK Output from transform
REMARK  STAMP Package (Russell and Barton Proteins, 14, 309-323, 1992)
REMARK Domains were read from the file ./domainalign-1234567890.1234.sort
REMARK Chains are labelled sequentially starting with 'A' and
REMARK  after the order given in the file ./domainalign-1234567890.1234.sort
REMARK The domains in this file are:
REMARK       d4at1b1  chain A 
REMARK       d4at1d1_1  chain B 
REMARK Does not include heteroatoms
REMARK  Does not include DNA/RNA 
REMARK Does not include waters
ATOM      1  N   GLY A   8      13.557  82.383  35.829  1.00 92.06           N  
ATOM      2  CA  GLY A   8      14.363  82.355  34.620  1.00 92.63           C  
ATOM      3  C   GLY A   8      14.480  83.797  34.150  1.00 91.80           C  
ATOM      4  O   GLY A   8      13.625  84.596  34.527  1.00 93.34           O  
ATOM      5  N   VAL A   9      15.499  84.132  33.352  1.00 90.04           N  
ATOM      6  CA  VAL A   9      15.799  85.525  33.008  1.00 89.55           C  
ATOM      7  C   VAL A   9      15.294  86.094  31.646  1.00 90.94           C  
ATOM      8  O   VAL A   9      14.395  85.528  31.008  1.00 91.46           O  
ATOM      9  CB  VAL A   9      17.381  85.731  33.167  1.00 88.13           C  
ATOM     10  CG1 VAL A   9      17.571  86.421  34.506  1.00 86.27           C  
ATOM     11  CG2 VAL A   9      18.232  84.456  33.191  1.00 86.95           C  
ATOM     12  N   GLU A  10      15.892  87.223  31.201  1.00 89.98           N  
ATOM     13  CA  GLU A  10      15.543  87.988  30.004  1.00 87.19           C  
ATOM     14  C   GLU A  10      16.748  88.251  29.055  1.00 83.25           C  
ATOM     15  O   GLU A  10      17.879  87.817  29.318  1.00 81.89           O  
ATOM     16  CB  GLU A  10      14.876  89.324  30.474  1.00 89.77           C  
ATOM     17  CG  GLU A  10      15.390  90.058  31.748  1.00 93.53           C  
ATOM     18  CD  GLU A  10      16.862  90.513  31.791  1.00 96.84           C  
ATOM     19  OE1 GLU A  10      17.570  90.129  32.731  1.00 98.75           O  
ATOM     20  OE2 GLU A  10      17.306  91.258  30.905  1.00 97.00           O  
ATOM     21  N   ALA A  11      16.471  89.023  27.987  1.00 77.76           N  
ATOM     22  CA  ALA A  11      17.315  89.379  26.829  1.00 71.32           C  
ATOM     23  C   ALA A  11      18.829  89.525  26.622  1.00 65.96           C  
ATOM     24  O   ALA A  11      19.605  90.124  27.370  1.00 64.35           O  
ATOM     25  CB  ALA A  11      16.692  90.608  26.193  1.00 70.48           C  
ATOM     26  N   ILE A  12      19.133  88.956  25.457  1.00 62.08           N  
ATOM     27  CA  ILE A  12      20.419  88.929  24.778  1.00 60.99           C  
ATOM     28  C   ILE A  12      19.984  89.116  23.325  1.00 61.87           C  
ATOM     29  O   ILE A  12      18.841  88.755  22.999  1.00 62.16           O  
ATOM     30  CB  ILE A  12      21.198  87.545  24.850  1.00 59.43           C  
ATOM     31  CG1 ILE A  12      20.354  86.363  24.347  1.00 55.38           C  
ATOM     32  CG2 ILE A  12      21.619  87.298  26.290  1.00 59.29           C  
ATOM     33  CD1 ILE A  12      21.107  85.072  24.029  1.00 50.25           C  
ATOM     34  N   LYS A  13      20.745  89.683  22.389  1.00 62.88           N  
ATOM     35  CA  LYS A  13      20.307  89.668  20.991  1.00 63.76           C  
ATOM     36  C   LYS A  13      21.229  88.611  20.439  1.00 63.26           C  
ATOM     37  O   LYS A  13      22.425  88.631  20.755  1.00 63.54           O  
ATOM     38  CB  LYS A  13      20.570  90.941  20.133  1.00 65.83           C  
ATOM     39  CG  LYS A  13      21.100  92.232  20.765  1.00 68.73           C  


  [Part of this file has been deleted for brevity]

ATOM    675  O   LYS B  94      12.693  74.657  17.434  1.00 60.00           O  
ATOM    676  CB  LYS B  94      11.413  76.088  20.143  1.00 54.56           C  
ATOM    677  CG  LYS B  94      10.900  77.250  20.960  1.00 56.83           C  
ATOM    678  CD  LYS B  94       9.921  76.669  21.989  1.00 59.11           C  
ATOM    679  CE  LYS B  94       9.042  77.715  22.639  1.00 60.10           C  
ATOM    680  NZ  LYS B  94       9.889  78.700  23.257  1.00 64.17           N  
ATOM    681  N   SER B  95      13.442  74.032  19.482  1.00 54.16           N  
ATOM    682  CA  SER B  95      13.784  72.649  19.193  1.00 49.80           C  
ATOM    683  C   SER B  95      13.766  71.902  20.529  1.00 49.50           C  
ATOM    684  O   SER B  95      13.714  72.493  21.615  1.00 50.66           O  
ATOM    685  CB  SER B  95      15.185  72.557  18.594  1.00 49.06           C  
ATOM    686  OG  SER B  95      15.486  73.548  17.613  1.00 48.30           O  
ATOM    687  N   ARG B  96      13.816  70.588  20.496  1.00 50.27           N  
ATOM    688  CA  ARG B  96      13.866  69.769  21.692  1.00 49.58           C  
ATOM    689  C   ARG B  96      14.838  68.645  21.293  1.00 47.31           C  
ATOM    690  O   ARG B  96      15.004  68.412  20.086  1.00 44.69           O  
ATOM    691  CB  ARG B  96      12.425  69.303  21.982  1.00 53.09           C  
ATOM    692  CG  ARG B  96      12.196  68.402  23.199  1.00 58.05           C  
ATOM    693  CD  ARG B  96      10.792  68.555  23.786  1.00 61.70           C  
ATOM    694  NE  ARG B  96      10.616  69.893  24.352  1.00 66.11           N  
ATOM    695  CZ  ARG B  96       9.771  70.813  23.848  1.00 69.37           C  
ATOM    696  NH1 ARG B  96       9.701  72.022  24.420  1.00 71.16           N  
ATOM    697  NH2 ARG B  96       8.986  70.556  22.788  1.00 70.99           N  
ATOM    698  N   PRO B  97      15.590  68.000  22.196  1.00 47.31           N  
ATOM    699  CA  PRO B  97      16.436  66.851  21.916  1.00 47.03           C  
ATOM    700  C   PRO B  97      15.753  65.608  21.356  1.00 46.69           C  
ATOM    701  O   PRO B  97      14.799  65.054  21.927  1.00 47.44           O  
ATOM    702  CB  PRO B  97      17.136  66.579  23.236  1.00 48.99           C  
ATOM    703  CG  PRO B  97      17.255  67.938  23.886  1.00 49.17           C  
ATOM    704  CD  PRO B  97      15.866  68.471  23.557  1.00 49.45           C  
ATOM    705  N   SER B  98      16.312  65.237  20.189  1.00 45.02           N  
ATOM    706  CA  SER B  98      16.014  64.020  19.435  1.00 41.65           C  
ATOM    707  C   SER B  98      17.196  63.099  19.710  1.00 39.46           C  
ATOM    708  O   SER B  98      18.326  63.606  19.716  1.00 38.78           O  
ATOM    709  CB  SER B  98      15.951  64.289  17.938  1.00 42.24           C  
ATOM    710  OG  SER B  98      14.655  64.742  17.585  1.00 46.01           O  
ATOM    711  N   LEU B  99      16.990  61.791  19.948  1.00 36.31           N  
ATOM    712  CA  LEU B  99      18.077  60.867  20.272  1.00 33.04           C  
ATOM    713  C   LEU B  99      19.003  60.690  19.049  1.00 33.65           C  
ATOM    714  O   LEU B  99      18.466  60.337  17.992  1.00 35.86           O  
ATOM    715  CB  LEU B  99      17.418  59.571  20.695  1.00 29.39           C  
ATOM    716  CG  LEU B  99      18.124  58.647  21.688  1.00 28.47           C  
ATOM    717  CD1 LEU B  99      18.259  59.350  23.047  1.00 27.24           C  
ATOM    718  CD2 LEU B  99      17.331  57.340  21.816  1.00 25.66           C  
ATOM    719  N   PRO B 100      20.323  60.969  19.039  1.00 33.12           N  
ATOM    720  CA  PRO B 100      21.144  60.883  17.828  1.00 35.17           C  
ATOM    721  C   PRO B 100      21.515  59.411  17.591  1.00 38.22           C  
ATOM    722  O   PRO B 100      21.546  58.618  18.541  1.00 36.98           O  
ATOM    723  CB  PRO B 100      22.316  61.774  18.141  1.00 34.28           C  
ATOM    724  CG  PRO B 100      22.528  61.462  19.624  1.00 33.62           C  
ATOM    725  CD  PRO B 100      21.122  61.358  20.202  1.00 31.93           C

Directory: daf

This directory contains output files, for example 54894.daf and 55074.daf.

File: daf/54894.daf

# TY   SCOP
# XX
# CL   Alpha and beta proteins (a+b)
# XX
# FO   Ferredoxin-like
# XX
# SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
# XX
# FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
# XX
# SI   54894
# XX
#         Number               10        20        30        40        50    
d4at1b1              0 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPXSGEMGRKDLIKIEN      0
d4at1d1              0 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGXEMGRKDLIKIEN      0
# Post_similar         111111111111111111111111111111111111111111-0-111111111111

#         Number        60        70        80        90 
d4at1b1              0 TFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP      0
d4at1d1              0 TFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP      0
# Post_similar         1111111111111111111111111111111111111

File: daf/55074.daf

# TY   SCOP
# XX
# CL   Alpha and beta proteins (a+b)
# XX
# FO   Ferredoxin-like
# XX
# SF   Adenylyl and guanylyl cyclase catalytic domain
# XX
# FA   Adenylyl and guanylyl cyclase catalytic domain
# XX
# SI   55074
# XX
#         Number               10        20        30        40        50    
d1cs4a_              0 MMFHKIYIQKXHXDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENH      0
d1fx2a_              0 XXNNNRAPXKEPTDPVTLIFTDIESSTALWAAXHPDLMPDAVAAHHRMVRSLIGRYK      0
# Post_similar         --000000-0-0-1111111111111111111-000111111111111111111111

#         Number        60        70        80        90       100       110 
d1cs4a_              0 CLRIKILGDCYYCVSGLPEARADHAHCCVEMGMDMIEAISLVREMXTXGXXXXXXXX      0
d1fx2a_              0 CYEVKTVGDSFMIAXXXXSKXXXSPFAAVQLAQELQLCFLHXHDWGTNALDDSYREF      0
# Post_similar         11111111111111----00---111111111111111111-000-0-0--------

#         Number          120       130       140       150       160       170
d1cs4a_              0 XXXXXXXXXXXXXXXXXXXXXXXXXXXVNVNMRVGIHSGRVHXCGVLGLRKWQFDVW      0
d1fx2a_              0 EEQRAEGECEYTPPTAHMDPEVYSRLWNGLRVRVGIHTGLCDIRHDXEXVTKGYDYY      0
# Post_similar         ---------------------------011111111111111-111-0-00001111

#         Number             180       190       200       210       220     
d1cs4a_              0 SNDVTLANHMEAGGKAGRIHITKATLSYLNXXXGXDYEVEPGCGGERNXAYLKEHSI      0
d1fx2a_              0 GRTPNMAARTESVANGGQVLMTHAAYMSLSAEDRKQIDVTALXGDXVALRGXVSDPV      0
# Post_similar         111111111111111111111111111111---0-1111111-00-00-00-00111

#         Number      230       240       250
d1cs4a_              0 ETFLILXXXXXXXXXXXXXXXXXX      0
d1fx2a_              0 KMYQLNTVPSRNFAALRLDREYFD      0
# Post_similar         111111------------------

File: 55074.ent

REMARK Output from transform
REMARK  STAMP Package (Russell and Barton Proteins, 14, 309-323, 1992)
REMARK Domains were read from the file ./domainalign-1234567890.1234.sort
REMARK Chains are labelled sequentially starting with 'A' and
REMARK  after the order given in the file ./domainalign-1234567890.1234.sort
REMARK The domains in this file are:
REMARK       d1cs4a_  chain A 
REMARK       d1fx2a__1  chain B 
REMARK Does not include heteroatoms
REMARK  Does not include DNA/RNA 
REMARK Does not include waters
ATOM      1  N   MET A 377      28.568 -27.770  32.255  1.00 73.77           N  
ATOM      2  CA  MET A 377      28.292 -26.443  32.794  1.00 72.28           C  
ATOM      3  C   MET A 377      29.325 -25.377  32.396  1.00 69.48           C  
ATOM      4  O   MET A 377      30.485 -25.687  32.098  1.00 67.04           O  
ATOM      5  CB  MET A 377      28.075 -26.504  34.312  1.00 74.79           C  
ATOM      6  CG  MET A 377      29.171 -27.205  35.092  1.00 78.73           C  
ATOM      7  SD  MET A 377      28.708 -27.446  36.824  1.00 83.74           S  
ATOM      8  CE  MET A 377      28.745 -25.745  37.440  1.00 81.94           C  
ATOM      9  N   MET A 378      28.883 -24.120  32.395  1.00 66.44           N  
ATOM     10  CA  MET A 378      29.698 -22.969  32.011  1.00 62.94           C  
ATOM     11  C   MET A 378      30.928 -22.727  32.886  1.00 59.70           C  
ATOM     12  O   MET A 378      32.059 -22.739  32.400  1.00 57.00           O  
ATOM     13  CB  MET A 378      28.824 -21.715  31.966  1.00 64.01           C  
ATOM     14  CG  MET A 378      27.551 -21.872  31.137  1.00 64.35           C  
ATOM     15  SD  MET A 378      27.897 -22.219  29.403  1.00 67.83           S  
ATOM     16  CE  MET A 378      27.844 -24.014  29.357  1.00 65.41           C  
ATOM     17  N   PHE A 379      30.697 -22.474  34.167  1.00 56.03           N  
ATOM     18  CA  PHE A 379      31.763 -22.225  35.123  1.00 53.16           C  
ATOM     19  C   PHE A 379      32.157 -23.501  35.837  1.00 51.53           C  
ATOM     20  O   PHE A 379      31.372 -24.440  35.914  1.00 53.09           O  
ATOM     21  CB  PHE A 379      31.296 -21.227  36.186  1.00 54.14           C  
ATOM     22  CG  PHE A 379      31.091 -19.832  35.671  1.00 51.13           C  
ATOM     23  CD1 PHE A 379      29.927 -19.493  34.986  1.00 50.12           C  
ATOM     24  CD2 PHE A 379      32.049 -18.846  35.907  1.00 49.63           C  
ATOM     25  CE1 PHE A 379      29.716 -18.196  34.546  1.00 51.63           C  
ATOM     26  CE2 PHE A 379      31.852 -17.545  35.474  1.00 50.16           C  
ATOM     27  CZ  PHE A 379      30.682 -17.216  34.792  1.00 51.72           C  
ATOM     28  N   HIS A 380      33.371 -23.529  36.372  1.00 50.09           N  
ATOM     29  CA  HIS A 380      33.830 -24.687  37.120  1.00 49.62           C  
ATOM     30  C   HIS A 380      33.046 -24.672  38.431  1.00 49.26           C  
ATOM     31  O   HIS A 380      32.579 -23.623  38.866  1.00 50.30           O  
ATOM     32  CB  HIS A 380      35.327 -24.574  37.439  1.00 52.29           C  
ATOM     33  CG  HIS A 380      36.235 -24.929  36.299  1.00 53.66           C  
ATOM     34  ND1 HIS A 380      36.782 -23.983  35.457  1.00 53.12           N  
ATOM     35  CD2 HIS A 380      36.737 -26.122  35.898  1.00 52.37           C  
ATOM     36  CE1 HIS A 380      37.581 -24.576  34.588  1.00 50.60           C  
ATOM     37  NE2 HIS A 380      37.572 -25.873  34.833  1.00 52.60           N  
ATOM     38  N   LYS A 381      32.879 -25.832  39.051  1.00 50.19           N  
ATOM     39  CA  LYS A 381      32.167 -25.897  40.318  1.00 51.93           C  


  [Part of this file has been deleted for brevity]

ATOM   1806  CG  ASP B1117      55.880   2.261  56.337  1.00 70.08           C  
ATOM   1807  OD1 ASP B1117      55.413   2.019  55.196  1.00 73.38           O  
ATOM   1808  OD2 ASP B1117      57.083   2.060  56.637  1.00 70.53           O  
ATOM   1809  N   ARG B1118      52.763   0.078  56.474  1.00 66.61           N  
ATOM   1810  CA  ARG B1118      52.480  -1.376  56.573  1.00 68.20           C  
ATOM   1811  C   ARG B1118      53.211  -2.510  55.827  1.00 68.77           C  
ATOM   1812  O   ARG B1118      54.420  -2.486  55.586  1.00 70.57           O  
ATOM   1813  CB  ARG B1118      51.032  -1.595  56.196  1.00 71.02           C  
ATOM   1814  CG  ARG B1118      49.987  -0.729  56.780  1.00 66.89           C  
ATOM   1815  CD  ARG B1118      48.804  -0.984  55.854  1.00 69.79           C  
ATOM   1816  NE  ARG B1118      47.547  -0.456  56.345  1.00 65.16           N  
ATOM   1817  CZ  ARG B1118      47.349   0.806  56.713  1.00 67.30           C  
ATOM   1818  NH1 ARG B1118      48.317   1.718  56.648  1.00 62.67           N  
ATOM   1819  NH2 ARG B1118      46.197   1.138  57.252  1.00 60.83           N  
ATOM   1820  N   GLU B1119      52.369  -3.489  55.467  1.00 74.62           N  
ATOM   1821  CA  GLU B1119      52.575  -4.774  54.755  1.00 71.44           C  
ATOM   1822  C   GLU B1119      51.215  -5.343  55.151  1.00 68.30           C  
ATOM   1823  O   GLU B1119      50.786  -5.070  56.254  1.00 70.28           O  
ATOM   1824  CB  GLU B1119      53.627  -5.681  55.450  1.00 72.63           C  
ATOM   1825  CG  GLU B1119      53.055  -6.990  56.216  1.00 68.78           C  
ATOM   1826  CD  GLU B1119      52.428  -6.727  57.621  1.00 67.37           C  
ATOM   1827  OE1 GLU B1119      52.887  -5.742  58.270  1.00 63.79           O  
ATOM   1828  OE2 GLU B1119      51.452  -7.442  58.066  1.00 24.30           O  
ATOM   1829  N   TYR B1120      50.503  -6.072  54.309  1.00 69.56           N  
ATOM   1830  CA  TYR B1120      49.236  -6.678  54.769  1.00 66.82           C  
ATOM   1831  C   TYR B1120      49.095  -7.990  54.006  1.00 69.41           C  
ATOM   1832  O   TYR B1120      49.546  -8.081  52.863  1.00 60.86           O  
ATOM   1833  CB  TYR B1120      48.062  -5.720  54.628  1.00 64.84           C  
ATOM   1834  CG  TYR B1120      46.959  -6.106  53.680  1.00 72.65           C  
ATOM   1835  CD1 TYR B1120      47.055  -5.808  52.324  1.00 69.04           C  
ATOM   1836  CD2 TYR B1120      45.764  -6.657  54.153  1.00 72.45           C  
ATOM   1837  CE1 TYR B1120      45.995  -6.037  51.460  1.00 74.31           C  
ATOM   1838  CE2 TYR B1120      44.687  -6.891  53.292  1.00 74.14           C  
ATOM   1839  CZ  TYR B1120      44.814  -6.575  51.946  1.00 77.01           C  
ATOM   1840  OH  TYR B1120      43.764  -6.790  51.086  1.00 73.74           O  
ATOM   1841  N   PHE B1121      48.537  -9.015  54.662  1.00 67.32           N  
ATOM   1842  CA  PHE B1121      48.400 -10.386  54.119  1.00 68.14           C  
ATOM   1843  C   PHE B1121      48.560 -10.743  52.625  1.00 68.72           C  
ATOM   1844  O   PHE B1121      49.617 -11.227  52.232  1.00 71.84           O  
ATOM   1845  CB  PHE B1121      47.209 -11.122  54.716  1.00 64.05           C  
ATOM   1846  CG  PHE B1121      47.407 -12.617  54.793  1.00 61.04           C  
ATOM   1847  CD1 PHE B1121      48.271 -13.163  55.733  1.00 58.84           C  
ATOM   1848  CD2 PHE B1121      46.736 -13.477  53.925  1.00 63.12           C  
ATOM   1849  CE1 PHE B1121      48.465 -14.539  55.814  1.00 60.74           C  
ATOM   1850  CE2 PHE B1121      46.924 -14.858  53.998  1.00 59.31           C  
ATOM   1851  CZ  PHE B1121      47.787 -15.391  54.940  1.00 64.18           C  
ATOM   1852  N   ASP B1122      47.527 -10.584  51.804  1.00 72.82           N  
ATOM   1853  CA  ASP B1122      47.655 -10.919  50.373  1.00 73.64           C  
ATOM   1854  C   ASP B1122      46.519 -10.364  49.515  1.00 74.17           C  
ATOM   1855  O   ASP B1122      46.463 -10.760  48.331  1.00 75.01           O  
ATOM   1856  CB  ASP B1122      47.789 -12.445  50.171  1.00 73.22           C

File: domainalign.log

Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'




5.0 DATA FILES

DOMAINALIGN does not use any data files but uses the STAMP "pdb.directories" file which specifies the permissible prefix, extension and path of PDB files used by STAMP. This file should look like : 
 test_data/ - .dent
 /data/pdb - -
 /data/pdb _ .ent
 /data/pdb _ .pdb
 /data/pdb pdb .ent
 /data/pdbscop _ _
 /data/pdbscop _ .ent
 /data/pdbscop _ .pdb
 /data/pdbscop pdb .ent
 ./ _ _
 ./ _ .ent
 ./ _ .ent.z
 ./ _ .ent.gz
 ./ _ .pdb
 ./ _ .pdb.Z
 ./ _ .pdb.gz
 ./ pdb .ent
 ./ pdb .ent.Z
 ./ pdb .ent.gz
 /data/CASS1/pdb/coords/ _ .pdb
 /data/CASS1/pdb/coords/ _ .pdb.Z
 /data/CASS1/pdb/coords/ _ .pdb.gz



6.0 USAGE

6.1 COMMAND LINE ARGUMENTS 

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-dcfinfile]         infile     This option specifies the name of DCF file
                                  (domain classification file) (input). A
                                  'domain classification file' contains
                                  classification and other data for domains
                                  from SCOP or CATH, in DCF format
                                  (EMBL-like). The files are generated by
                                  using SCOPPARSE and CATHPARSE. Domain
                                  sequence information can be added to the
                                  file by using DOMAINSEQS.
  [-pdbdir]            directory  [./] This option specifies the location of
                                  domain PDB files (input). A 'domain PDB
                                  file' contains coordinate data for a single
                                  domain from SCOP or CATH, in PDB format. The
                                  files are generated by using DOMAINER.
   -node               menu       [1] This option specifies the node for
                                  redundancy removal. Redundancy can be
                                  removed at any specified node in the SCOP or
                                  CATH hierarchies. For example by selecting
                                  'Class' entries belonging to the same Class
                                  will be non-redundant. (Values: 1 (Class
                                  (SCOP)); 2 (Fold (SCOP)); 3 (Superfamily
                                  (SCOP)); 4 (Family (SCOP)); 5 (Class
                                  (CATH)); 6 (Architecture (CATH)); 7
                                  (Topology (CATH)); 8 (Homologous Superfamily
                                  (CATH)); 9 (Family (CATH)))
   -mode               menu       [1] This option specifies the alignment
                                  algorithm to use. (Values: 1 (STAMP); 2
                                  (TCOFFEE))
   -[no]keepsinglets   toggle     [Y] This option specifies whether to write
                                  sequences of singlet families to file. If
                                  you specify this option, the sequence for
                                  each singlet family are written to file
                                  (output).
  [-dafoutdir]         outdir     [./] This option specifies the location of
                                  DAF files (domain alignment files) (output).
                                  A 'domain alignment file' contains a
                                  sequence alignment of domains belonging to
                                  the same SCOP or CATH family. The files are
                                  in clustal format and are annotated with
                                  domain family classification information.
                                  The files generated by using SCOPALIGN will
                                  contain a structure-based sequence alignment
                                  of domains of known structure only. Such
                                  alignments can be extended with sequence
                                  relatives (of unknown structure) by using
                                  SEQALIGN.
*  -singletsoutdir     outdir     [./] This option specifies the location of
                                  DHF files (domain hits files) for singlet
                                  sequences (output). The singlets are written
                                  out as a 'domain hits file' - which
                                  contains database hits (sequences) with
                                  domain classification information, in FASTA
                                  format.
*  -superoutdir        outdir     [./] This option specifies the location of
                                  structural superimposition files (output). A
                                  file in PDB format of the structural
                                  superimposition is generated for each family
                                  if the STAMP algorithm is used.
   -logfile            outfile    [domainalign.log] This option specifies the
                                  name of log file (output). The log file
                                  contains messages about any errors arising
                                  while domainalign ran.

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-logfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Standard (Mandatory) qualifiers Allowed values Default
[-dcfinfile]
(Parameter 1)		 This option specifies the name of DCF file (domain classification file) (input). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE and CATHPARSE. Domain sequence information can be added to the file by using DOMAINSEQS. Input file Required
[-pdbdir]
(Parameter 2)		 This option specifies the location of domain PDB files (input). A 'domain PDB file' contains coordinate data for a single domain from SCOP or CATH, in PDB format. The files are generated by using DOMAINER. Directory ./
-node This option specifies the node for redundancy removal. Redundancy can be removed at any specified node in the SCOP or CATH hierarchies. For example by selecting 'Class' entries belonging to the same Class will be non-redundant.
1 (Class (SCOP))
2 (Fold (SCOP))
3 (Superfamily (SCOP))
4 (Family (SCOP))
5 (Class (CATH))
6 (Architecture (CATH))
7 (Topology (CATH))
8 (Homologous Superfamily (CATH))
9 (Family (CATH))
 1
-mode This option specifies the alignment algorithm to use.
1 (STAMP)
2 (TCOFFEE)
 1
-[no]keepsinglets This option specifies whether to write sequences of singlet families to file. If you specify this option, the sequence for each singlet family are written to file (output). Toggle value Yes/No Yes
[-dafoutdir]
(Parameter 3)		 This option specifies the location of DAF files (domain alignment files) (output). A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The files are in clustal format and are annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. Output directory ./
-singletsoutdir This option specifies the location of DHF files (domain hits files) for singlet sequences (output). The singlets are written out as a 'domain hits file' - which contains database hits (sequences) with domain classification information, in FASTA format. Output directory ./
-superoutdir This option specifies the location of structural superimposition files (output). A file in PDB format of the structural superimposition is generated for each family if the STAMP algorithm is used. Output directory ./
-logfile This option specifies the name of log file (output). The log file contains messages about any errors arising while domainalign ran. Output file domainalign.log
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
(none)

6.2 EXAMPLE SESSION

An example of interactive use of DOMAINALIGN is shown below. Here is a sample session with domainalign 


% domainalign 
Generate alignments (DAF file) for nodes in a DCF file.
Domain classification file: all.scop2
Domain pdb directory [./]: 
Node at which to remove redundancy
         1 : Class (SCOP)
         2 : Fold (SCOP)
         3 : Superfamily (SCOP)
         4 : Family (SCOP)
         5 : Class (CATH)
         6 : Architecture (CATH)
         7 : Topology (CATH)
         8 : Homologous Superfamily (CATH)
         9 : Family (CATH)
Select number. [1]: 4
Alignment algorithm option
         1 : STAMP
         2 : TCOFFEE
Select number. [1]: 1
Write sequences of singlet families to file. [Y]: N
Domain alignment file output directory [./]: daf
Pdb entry file output directory [./]: 
Domainatrix log output file [domainalign.log]: 


STAMP Structural Alignment of Multiple Proteins
 by Robert B. Russell & Geoffrey J. Barton 
 Please cite PROTEINS, v14, 309-323, 1992

Results of scan will be written to file ./domainalign-1234567890.1234.scan
Fits  = no. of fits performed, Sc = STAMP score, RMS = RMS deviation
Align = alignment length, Nfit = residues fitted, Eq. = equivalent residues
Secs  = no. equiv. secondary structures, %I = seq. identity, %S = sec. str. identity
P(m)  = P value (p=1/10) calculated after Murzin (1993), JMB, 230, 689-694

     Domain1         Domain2          Fits  Sc      RMS   Len1 Len2 Align Fit   Eq. Secs    %I    %S     P(m)
Scan d1cs4a_         d1cs4a_            1   9.799   0.001  189  189  189  189  188    0 100.00 100.00 0.00e+00
Scan d1cs4a_         d1fx2a_            1   6.522   1.343  189  235  225  135  133    0  20.30 100.00 0.00017
See the file ./domainalign-1234567890.1234.scan

stamp -l ./domainalign-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainalign-1234567890.1234 -d ./domainalign-1234567890.1234.set


sorttrans -f ./domainalign-1234567890.1234.scan -s Sc 2.5 > ./domainalign-1234567890.1234.sort


stamp -l ./domainalign-1234567890.1234.sort -prefix ./domainalign-1234567890.1234 > ./domainalign-1234567890.1234.log

TRANSFORM R.B. Russell, 1995
 Using PDB files
 Files will not include heteroatoms
 Files will not include DNA/RNA 
 Files will not include waters
 All coordinates will be in file ./55074.ent
 Domain   1, d1cs4a_ => to ./55074.ent (chain A)
 Domain   2, d1fx2a__1 => to ./55074.ent (chain B)
POSTSTAMP, R.B. Russell 1995
 New output will be in file ./domainalign-1234567890.1234.1
 E1 =   3.800, E2 =   3.800
 Minimum Pij set to 0.500
 Reading domain descriptors/transformations from the file ./domainalign-1234567890.1234.1
 Reading alignment...
  Reading coordinates...
 Domain   1 /homes/user/test/qa/domainer-keep2//d1cs4a_.ent d1cs4a_
        all residues 189 CAs =>  189 CAs in total
 Transforming coordinates...
 Domain   2 /homes/user/test/qa/domainer-keep2//d1fx2a_.ent d1fx2a__1
        all residues 235 CAs =>  235 CAs in total
 Transforming coordinates...
 ...done.

transform -f ./domainalign-1234567890.1234.sort -g  -o ./55074.ent

poststamp -f ./domainalign-1234567890.1234.1 -min 0.5

ver2hor -f ./domainalign-1234567890.1234.1.post > ./domainalign-1234567890.1234.out


STAMP Structural Alignment of Multiple Proteins
 by Robert B. Russell & Geoffrey J. Barton 
 Please cite PROTEINS, v14, 309-323, 1992

Results of scan will be written to file ./domainalign-1234567890.1234.scan
Fits  = no. of fits performed, Sc = STAMP score, RMS = RMS deviation
Align = alignment length, Nfit = residues fitted, Eq. = equivalent residues
Secs  = no. equiv. secondary structures, %I = seq. identity, %S = sec. str. identity
P(m)  = P value (p=1/10) calculated after Murzin (1993), JMB, 230, 689-694

     Domain1         Domain2          Fits  Sc      RMS   Len1 Len2 Align Fit   Eq. Secs    %I    %S     P(m)
Scan d4at1b1         d4at1b1            1   9.799   0.001   93   93   93   93   92    0 100.00 100.00 1.00e-92
Scan d4at1b1         d4at1d1            1   9.250   0.588   93   93   94   89   88    0 100.00 100.00 1.00e-88
See the file ./domainalign-1234567890.1234.scan

Processing node 54894

stamp -l ./domainalign-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainalign-1234567890.1234 -d ./domainalign-1234567890.1234.set


sorttrans -f ./domainalign-1234567890.1234.scan -s Sc 2.5 > ./domainalign-1234567890.1234.sort


stamp -l ./domainalign-1234567890.1234.sort -prefix ./domainalign-1234567890.1234 > ./domainalign-1234567890.1234.log

TRANSFORM R.B. Russell, 1995
 Using PDB files
 Files will not include heteroatoms
 Files will not include DNA/RNA 
 Files will not include waters
 All coordinates will be in file ./54894.ent
 Domain   1, d4at1b1 => to ./54894.ent (chain A)
 Domain   2, d4at1d1_1 => to ./54894.ent (chain B)
POSTSTAMP, R.B. Russell 1995
 New output will be in file ./domainalign-1234567890.1234.1
 E1 =   3.800, E2 =   3.800
 Minimum Pij set to 0.500
 Reading domain descriptors/transformations from the file ./domainalign-1234567890.1234.1
 Reading alignment...
  Reading coordinates...
 Domain   1 /homes/user/test/qa/domainer-keep2//d4at1b1.ent d4at1b1
        all residues  93 CAs =>   93 CAs in total
 Transforming coordinates...
 Domain   2 /homes/user/test/qa/domainer-keep2//d4at1d1.ent d4at1d1_1
        all residues  93 CAs =>   93 CAs in total
 Transforming coordinates...
 ...done.

transform -f ./domainalign-1234567890.1234.sort -g  -o ./54894.ent

poststamp -f ./domainalign-1234567890.1234.1 -min 0.5

ver2hor -f ./domainalign-1234567890.1234.1.post > ./domainalign-1234567890.1234.out

Go to the input files for this example
Go to the output files for this example



The following command line would achieve the same result. 
 
 domainalign /test_data/all.scop2 /test_data/ /test_data/ /test_data/domainalign -keepsinglets Y 
-singlets /test_data/domainalign -node 4 -mode 1
-->


7.0 KNOWN BUGS & WARNINGS

1. Use of stamp
DOMAINALIGN requires a modified version of STAMP (see Notes below). The modified STAMP application must be installed on the system that is running DOMAINALIGN.

2. Strange STAMP behaviour
STAMP will ignore (omit from the alignment and *not* replace with '-' or any other symbol) ANY residues or groups in a PDB file that

(i) are not structured (i.e. do not appear in the ATOM records) or
(ii) lack a CA atom, regardless of whether it is a known amino acid or not.

This means that the position (column) in the alignment cannot reliably be used as the basis for an index into arrays representing the full length sequences. STAMP will however include in the alignment residues with a single atom only, so long as it is the CA atom.

3. Handling of singlet nodes
No sequence alignment or structural superimposition files are generated for nodes that contain a single domain only. Sequences for such domains can be saved to file (see 2.0 INPUTS & OUTPUTS).

4. Alignment numbering
Residue number positions in alignment are not implemented (zero's are given).


8.0 NOTES

1. Adaption of STAMP for domain codes
DOMAINALIGN will only run with with a version of STAMP which has been modified so that PDB id codes of length greater than 4 characters are acceptable. This involves a trivial change to the STAMP module getdomain.c (around line number 155), a 4 must be changed to a 7 as follows: 
 temp=getfile(domain[0].id,dirfile,4,OUTPUT); 
 temp=getfile(domain[0].id,dirfile,7,OUTPUT);

2. Adaption of STAMP for larger datasets
STAMP fails to align a large dataset of all the available V set Ig domains. The ver2hor module generates the following error: 
 Transforming coordinates...
  ...done.
 ver2hor -f ./domainalign-1022069396.11280.76.post > ./domainalign-1022069396.11280.out
 error: something wrong with STAMP file
          STAMP length is 370, Alignment length is 422
          STAMP nseq is 155, Alignment nseq is 155

This is fixed by the following change in alignfit.h. 
#define MAXtlen 200 
#define MAXtlen 2000

At the same time the following may be changed as a safety measure: 
 gstamp.c  : #define MAX_SEQ_LEN 10000    (was 2000)
 pdbseq.c  : #define MAX_SEQ_LEN 10000    (was 3000)
 defaults.h: #define MAX_SEQ_LEN 10000    (was 8000)
 defaults.h: #define MAX_NSEQ 10000       (was 1000)
 defaults.h: #define MAX_BLOC_SEQ 5000    (was 500)
 dstamp.h  : #define MAX_N_SEQ 10000      (was 1000)
 ver2hor.h : #define MAX_N_SEQ 10000      (was 1000)


3. pdb.directories file
STAMP (and therefore DOMAINALIGN) uses a "pdb.directories" file: see 5.0 DATA FILES

4. Choice of alignment algorithm
Future versions of DOMAINALIGN will implement a larger choice of alignment algorithms.

5. Getting the best alignment
DOMAINALIGN will produce better alignments if the DCF file is reordered so that the representative structure of each node (e.g. family) is given first. This is achieved by using DOMAINREP.

6. Whitespace in alignment
STAMP can insert non-sensical whitespaces into its alignments, e.g. instead of a residue character where that residue was missing electron density in the PDB file. DOMAINALIGN replaces each whitespace within a STAMP alignment with an "X".

8.1 GLOSSARY OF FILE TYPES

FILE TYPE FORMAT DESCRIPTION CREATED BY SEE ALSO
Domain classification file (for SCOP) DCF format (EMBL-like format for domain classification data). Classification and other data for domains from SCOP. SCOPPARSE Domain sequence information can be added to the file by using DOMAINSEQS.
Domain classification file (for CATH) DCF format (EMBL-like format for domain classification data). Classification and other data for domains from CATH. CATHPARSE Domain sequence information can be added to the file by using DOMAINSEQS.
Domain PDB file PDB format for domain coordinate data. Coordinate data for a single domain from SCOP or CATH. DOMAINER N.A.
Domain alignment file DAF format (clustal format with domain classification information). Contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is annotated with domain family classification information. DOMAINALIGN (structure-based sequence alignment of domains of known structure). DOMAINALIGN alignments can be extended with sequence relatives (of unknown structure) to the family in question by using SEQALIGN.
None


9.0 DESCRIPTION

The generation of alignments for large datasets such as SCOP and CATH potentially requires a lot of time for preparation of datasets, writing of scripts, running individual jobs and so on, in addition to the compute time required for the alignments themselves. DOMAINALIGN automates this process: it reads a domain classification file and generates alignments for each user-specified node in turn.


10.0 ALGORITHM

More information on STAMP can be found at http://www.compbio.dundee.ac.uk/manuals/stamp.4.2
More information on TCOFFEE can be found at http://www.ch.embnet.org/software/TCoffee.html


11.0 RELATED APPLICATIONS

See also

Program name Description
contacts Generate intra-chain CON files from CCF files
domainrep Reorder DCF file to identify representative structures
domainreso Remove low resolution domains from a DCF file
interface Generate inter-chain CON files from CCF files
libgen Generate discriminating elements from alignments
matgen3d Generate a 3D-1D scoring matrix from CCF files
psiphi Calculates phi and psi torsion angles from protein coordinates
rocon Generates a hits file from comparing two DHF files
rocplot Performs ROC analysis on hits files
seqalign Extend alignments (DAF file) with sequences (DHF file)
seqfraggle Removes fragment sequences from DHF files
seqsearch Generate PSI-BLAST hits (DHF file) from a DAF file
seqsort Remove ambiguous classified sequences from DHF files
seqwords Generates DHF files from keyword search of UniProt
siggen Generates a sparse protein signature from an alignment
siggenlig Generates ligand-binding signatures from a CON file
sigscan Generates hits (DHF file) from a signature search
sigscanlig Searches ligand-signature library & writes hits (LHF file)



12.0 DIAGNOSTIC ERROR MESSAGES

The following message may appear in the log file.

Replaced ' ' in STAMP alignment with 'X' (STAMP can insert non-sensical whitespaces into its alignments, e.g. instead of a residue character where that residue was missing electron density in the PDB file. DOMAINALIGN replaces each whitespace within a STAMP alignment with an "X").


13.0 AUTHORS

Ranjeeva Ranasinghe

Jon Ison (jison@ebi.ac.uk)
The European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD UK


14.0 REFERENCES

Please cite the authors and EMBOSS.

Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European Molecular Biology Open Software Suite" Trends in Genetics, 15:276-278.

See also http://emboss.sourceforge.net/

14.1 Other useful references


Russell, R. B. & Barton, G. J. (1992), Multiple Sequence Alignment from Tertiary Structure Comparison: Assignment of Global and Residue Confidence Levels, PROTEINS: Struct. Funct. Genet., 14, 309-323.
C. Notredame, D. Higgins, J. Heringa. T-Coffee: A novel method for multiple sequence alignments. Journal of Molecular Biology, 302, 205-217, (2000)

More information on STAMP can be found at http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/
More information on TCOFFEE can be found at http://www.ch.embnet.org/software/TCoffee.html