
                         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-1121266435.25929.sort
REMARK Chains are labelled sequentially starting with 'A' and
REMARK  after the order given in the file ./domainalign-1121266435.25929.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      12.694  74.659  17.436  1.00 60.00           O

ATOM    676  CB  LYS B  94      11.414  76.090  20.144  1.00 54.56           C

ATOM    677  CG  LYS B  94      10.901  77.252  20.962  1.00 56.83           C

ATOM    678  CD  LYS B  94       9.923  76.671  21.990  1.00 59.11           C

ATOM    679  CE  LYS B  94       9.043  77.717  22.641  1.00 60.10           C

ATOM    680  NZ  LYS B  94       9.890  78.702  23.259  1.00 64.17           N

ATOM    681  N   SER B  95      13.444  74.034  19.484  1.00 54.16           N

ATOM    682  CA  SER B  95      13.785  72.651  19.195  1.00 49.80           C

ATOM    683  C   SER B  95      13.767  71.904  20.531  1.00 49.50           C

ATOM    684  O   SER B  95      13.715  72.494  21.617  1.00 50.66           O

ATOM    685  CB  SER B  95      15.186  72.559  18.595  1.00 49.06           C

ATOM    686  OG  SER B  95      15.488  73.550  17.615  1.00 48.30           O

ATOM    687  N   ARG B  96      13.817  70.590  20.497  1.00 50.27           N

ATOM    688  CA  ARG B  96      13.868  69.771  21.694  1.00 49.58           C

ATOM    689  C   ARG B  96      14.839  68.647  21.295  1.00 47.31           C

ATOM    690  O   ARG B  96      15.006  68.414  20.088  1.00 44.69           O

ATOM    691  CB  ARG B  96      12.426  69.305  21.983  1.00 53.09           C

ATOM    692  CG  ARG B  96      12.197  68.404  23.200  1.00 58.05           C

ATOM    693  CD  ARG B  96      10.794  68.557  23.787  1.00 61.70           C

ATOM    694  NE  ARG B  96      10.618  69.895  24.354  1.00 66.11           N

ATOM    695  CZ  ARG B  96       9.772  70.814  23.850  1.00 69.37           C

ATOM    696  NH1 ARG B  96       9.702  72.024  24.422  1.00 71.16           N

ATOM    697  NH2 ARG B  96       8.988  70.558  22.790  1.00 70.99           N

ATOM    698  N   PRO B  97      15.591  68.002  22.198  1.00 47.31           N

ATOM    699  CA  PRO B  97      16.438  66.853  21.917  1.00 47.03           C

ATOM    700  C   PRO B  97      15.755  65.610  21.357  1.00 46.69           C

ATOM    701  O   PRO B  97      14.800  65.056  21.929  1.00 47.44           O

ATOM    702  CB  PRO B  97      17.138  66.581  23.238  1.00 48.99           C

ATOM    703  CG  PRO B  97      17.256  67.940  23.887  1.00 49.17           C

ATOM    704  CD  PRO B  97      15.868  68.473  23.559  1.00 49.45           C

ATOM    705  N   SER B  98      16.313  65.239  20.191  1.00 45.02           N

ATOM    706  CA  SER B  98      16.016  64.022  19.436  1.00 41.65           C

ATOM    707  C   SER B  98      17.197  63.101  19.711  1.00 39.46           C

ATOM    708  O   SER B  98      18.327  63.608  19.718  1.00 38.78           O

ATOM    709  CB  SER B  98      15.952  64.291  17.940  1.00 42.24           C

ATOM    710  OG  SER B  98      14.657  64.744  17.586  1.00 46.01           O

ATOM    711  N   LEU B  99      16.992  61.793  19.950  1.00 36.31           N

ATOM    712  CA  LEU B  99      18.078  60.869  20.273  1.00 33.04           C

ATOM    713  C   LEU B  99      19.004  60.692  19.051  1.00 33.65           C

ATOM    714  O   LEU B  99      18.467  60.339  17.994  1.00 35.86           O

ATOM    715  CB  LEU B  99      17.420  59.573  20.697  1.00 29.39           C

ATOM    716  CG  LEU B  99      18.126  58.649  21.690  1.00 28.47           C

ATOM    717  CD1 LEU B  99      18.261  59.352  23.048  1.00 27.24           C

ATOM    718  CD2 LEU B  99      17.332  57.342  21.817  1.00 25.66           C

ATOM    719  N   PRO B 100      20.325  60.971  19.041  1.00 33.12           N

ATOM    720  CA  PRO B 100      21.146  60.885  17.830  1.00 35.17           C

ATOM    721  C   PRO B 100      21.517  59.413  17.592  1.00 38.22           C

ATOM    722  O   PRO B 100      21.547  58.620  18.542  1.00 36.98           O

ATOM    723  CB  PRO B 100      22.317  61.776  18.143  1.00 34.28           C

ATOM    724  CG  PRO B 100      22.530  61.464  19.626  1.00 33.62           C

ATOM    725  CD  PRO B 100      21.124  61.360  20.204  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 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPXSGEMGRKDLIKIE
N      0
d4at1d1              0 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGXEMGRKDLIKIE
N      0
# Post_similar         111111111111111111111111111111111111111111-0-11111111111
1

#         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 MMFHKIYIQKXHXDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAEN
H      0
d1fx2a_              0 XXNNNRAPXKEPTDPVTLIFTDIESSTALWAAXHPDLMPDAVAAHHRMVRSLIGRY
K      0
# Post_similar         --000000-0-0-1111111111111111111-00011111111111111111111
1

#         Number        60        70        80        90       100       110
d1cs4a_              0 CLRIKILGDCYYCVSGLPEARADHAHCCVEMGMDMIEAISLVREMXTXGXXXXXXX
X      0
d1fx2a_              0 CYEVKTVGDSFMIAXXXXSKXXXSPFAAVQLAQELQLCFLHXHDWGTNALDDSYRE
F      0
# Post_similar         11111111111111----00---111111111111111111-000-0-0-------
-

#         Number          120       130       140       150       160       170
d1cs4a_              0 XXXXXXXXXXXXXXXXXXXXXXXXXXXVNVNMRVGIHSGRVHXCGVLGLRKWQFDV
W      0
d1fx2a_              0 EEQRAEGECEYTPPTAHMDPEVYSRLWNGLRVRVGIHTGLCDIRHDXEXVTKGYDY
Y      0
# Post_similar         ---------------------------011111111111111-111-0-0000111
1

#         Number             180       190       200       210       220
d1cs4a_              0 SNDVTLANHMEAGGKAGRIHITKATLSYLNXXXGXDYEVEPGCGGERNXAYLKEHS
I      0
d1fx2a_              0 GRTPNMAARTESVANGGQVLMTHAAYMSLSAEDRKQIDVTALXGDXVALRGXVSDP
V      0
# Post_similar         111111111111111111111111111111---0-1111111-00-00-00-0011
1

#         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-1121266435.25929.sort
REMARK Chains are labelled sequentially starting with 'A' and
REMARK  after the order given in the file ./domainalign-1121266435.25929.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      55.881   2.260  56.337  1.00 70.08           C

ATOM   1807  OD1 ASP B1117      55.414   2.017  55.197  1.00 73.38           O

ATOM   1808  OD2 ASP B1117      57.084   2.059  56.637  1.00 70.53           O

ATOM   1809  N   ARG B1118      52.764   0.077  56.474  1.00 66.61           N

ATOM   1810  CA  ARG B1118      52.481  -1.377  56.573  1.00 68.20           C

ATOM   1811  C   ARG B1118      53.212  -2.511  55.828  1.00 68.77           C

ATOM   1812  O   ARG B1118      54.421  -2.488  55.587  1.00 70.57           O

ATOM   1813  CB  ARG B1118      51.033  -1.596  56.196  1.00 71.02           C

ATOM   1814  CG  ARG B1118      49.988  -0.730  56.780  1.00 66.89           C

ATOM   1815  CD  ARG B1118      48.805  -0.985  55.855  1.00 69.79           C

ATOM   1816  NE  ARG B1118      47.548  -0.457  56.346  1.00 65.16           N

ATOM   1817  CZ  ARG B1118      47.350   0.805  56.714  1.00 67.30           C

ATOM   1818  NH1 ARG B1118      48.318   1.717  56.649  1.00 62.67           N

ATOM   1819  NH2 ARG B1118      46.198   1.137  57.253  1.00 60.83           N

ATOM   1820  N   GLU B1119      52.370  -3.490  55.468  1.00 74.62           N

ATOM   1821  CA  GLU B1119      52.576  -4.775  54.756  1.00 71.44           C

ATOM   1822  C   GLU B1119      51.216  -5.345  55.152  1.00 68.30           C

ATOM   1823  O   GLU B1119      50.787  -5.071  56.255  1.00 70.28           O

ATOM   1824  CB  GLU B1119      53.628  -5.683  55.451  1.00 72.63           C

ATOM   1825  CG  GLU B1119      53.056  -6.991  56.217  1.00 68.78           C

ATOM   1826  CD  GLU B1119      52.428  -6.728  57.622  1.00 67.37           C

ATOM   1827  OE1 GLU B1119      52.888  -5.743  58.270  1.00 63.79           O

ATOM   1828  OE2 GLU B1119      51.452  -7.444  58.067  1.00 24.30           O

ATOM   1829  N   TYR B1120      50.504  -6.074  54.309  1.00 69.56           N

ATOM   1830  CA  TYR B1120      49.237  -6.679  54.769  1.00 66.82           C

ATOM   1831  C   TYR B1120      49.096  -7.992  54.006  1.00 69.41           C

ATOM   1832  O   TYR B1120      49.547  -8.082  52.863  1.00 60.86           O

ATOM   1833  CB  TYR B1120      48.062  -5.721  54.629  1.00 64.84           C

ATOM   1834  CG  TYR B1120      46.960  -6.107  53.681  1.00 72.65           C

ATOM   1835  CD1 TYR B1120      47.056  -5.809  52.324  1.00 69.04           C

ATOM   1836  CD2 TYR B1120      45.764  -6.658  54.154  1.00 72.45           C

ATOM   1837  CE1 TYR B1120      45.996  -6.038  51.461  1.00 74.31           C

ATOM   1838  CE2 TYR B1120      44.688  -6.892  53.292  1.00 74.14           C

ATOM   1839  CZ  TYR B1120      44.815  -6.576  51.947  1.00 77.01           C

ATOM   1840  OH  TYR B1120      43.765  -6.791  51.087  1.00 73.74           O

ATOM   1841  N   PHE B1121      48.537  -9.016  54.663  1.00 67.32           N

ATOM   1842  CA  PHE B1121      48.401 -10.387  54.120  1.00 68.14           C

ATOM   1843  C   PHE B1121      48.561 -10.745  52.626  1.00 68.72           C

ATOM   1844  O   PHE B1121      49.618 -11.228  52.233  1.00 71.84           O

ATOM   1845  CB  PHE B1121      47.210 -11.123  54.717  1.00 64.05           C

ATOM   1846  CG  PHE B1121      47.408 -12.619  54.794  1.00 61.04           C

ATOM   1847  CD1 PHE B1121      48.271 -13.164  55.734  1.00 58.84           C

ATOM   1848  CD2 PHE B1121      46.737 -13.479  53.925  1.00 63.12           C

ATOM   1849  CE1 PHE B1121      48.466 -14.540  55.815  1.00 60.74           C

ATOM   1850  CE2 PHE B1121      46.925 -14.859  53.999  1.00 59.31           C

ATOM   1851  CZ  PHE B1121      47.788 -15.392  54.941  1.00 64.18           C

ATOM   1852  N   ASP B1122      47.527 -10.585  51.805  1.00 72.82           N

ATOM   1853  CA  ASP B1122      47.656 -10.920  50.374  1.00 73.64           C

ATOM   1854  C   ASP B1122      46.520 -10.365  49.515  1.00 74.17           C

ATOM   1855  O   ASP B1122      46.464 -10.761  48.332  1.00 75.01           O

ATOM   1856  CB  ASP B1122      47.790 -12.446  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. On the RFCGR system,
   this file is /packages/stamp/defs/pdb.directories and 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       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.
   -mode               menu       This option specifies the alignment
                                  algorithm to use.
   -[no]keepsinglets   toggle     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    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 standard output
   -filter             boolean    Read standard input, write 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 deaths


   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.
Name of DCF file (domain classification file) (input).: all.scop2
Location of domain PDB files (input). [./]: ../domainer-keep2
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
Location of DAF files (domain alignment files) (output). [./]: daf
Location of structural superimposition files (output). [./]: 
Name of log file (output). [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-1121266435.25929.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. ide
ntity
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-1121266435.25929.scan
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-1121266435.25929.1
 E1 =   3.800, E2 =   3.800
 Minimum Pij set to 0.500
 Reading domain descriptors/transformations from the file ./domainalign-1121266
435.25929.1
 Reading alignment...
  Reading coordinates...
 Domain   1 ../domainer-keep2//d1cs4a_.ent d1cs4a_
        all residues 189 CAs =>  189 CAs in total
 Transforming coordinates...
 Domain   2 ../domainer-keep2//d1fx2a_.ent d1fx2a__1
        all residues 235 CAs =>  235 CAs in total
 Transforming coordinates...
 ...done.

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-1121266435.25929.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. ide
ntity
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   9.251   0.588   93   93   94   89
 88    0 100.00 100.00 1.00e-88
See the file ./domainalign-1121266435.25929.scan
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-1121266435.25929.1
 E1 =   3.800, E2 =   3.800
 Minimum Pij set to 0.500
 Reading domain descriptors/transformations from the file ./domainalign-1121266
435.25929.1
 Reading alignment...
  Reading coordinates...
 Domain   1 ../domainer-keep2//d4at1b1.ent d4at1b1
        all residues  93 CAs =>   93 CAs in total
 Transforming coordinates...
 Domain   2 ../domainer-keep2//d4at1d1.ent d4at1d1_1
        all residues  93 CAs =>   93 CAs in total
 Transforming coordinates...
 ...done.

stamp -l ./domainalign-1121266435.25929.dom -s -n 2 -slide 5 -prefix ./domainal
ign-1121266435.25929 -d ./domainalign-1121266435.25929.set


sorttrans -f ./domainalign-1121266435.25929.scan -s Sc 2.5 > ./domainalign-1121
266435.25929.sort


stamp -l ./domainalign-1121266435.25929.sort -prefix ./domainalign-1121266435.2
5929 > ./domainalign-1121266435.25929.log


transform -f ./domainalign-1121266435.25929.sort -g  -o ./55074.ent

poststamp -f ./domainalign-1121266435.25929.1 -min 0.5

ver2hor -f ./domainalign-1121266435.25929.1.post > ./domainalign-1121266435.259
29.out


Processing node 54894

stamp -l ./domainalign-1121266435.25929.dom -s -n 2 -slide 5 -prefix ./domainal
ign-1121266435.25929 -d ./domainalign-1121266435.25929.set


sorttrans -f ./domainalign-1121266435.25929.scan -s Sc 2.5 > ./domainalign-1121
266435.25929.sort


stamp -l ./domainalign-1121266435.25929.sort -prefix ./domainalign-1121266435.2
5929 > ./domainalign-1121266435.25929.log


transform -f ./domainalign-1121266435.25929.sort -g  -o ./54894.ent

poststamp -f ./domainalign-1121266435.25929.1 -min 0.5

ver2hor -f ./domainalign-1121266435.25929.1.post > ./domainalign-1121266435.259
29.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/domainalig
n -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.
   When running DOMAINALIGN at the RFCGR, to ensure the modified version
   of STAMP is used, type 'use stamp2' (which runs the script
   /packages/menu/USE/stamp2) before DOMAINALIGN is run.
   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-1022069396.1
1280.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)

   The modified code (for 2. and 3. above) is kept on the HGMP file
   system in /packages/stamp/src2
   WHEN RUNNING DOMAINALIGN AT THE HGMP IT IS ESSENTIAL THAT THE COMMAND
   'use stamp2' (which runs the script /packages/menu/USE/stamp2) IS
   GIVEN BEFORE DOMAINALIGN IS RUN. 
   This will ensure that the modified version of STAMP is used.
   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
   contactcount Count specific versus non-specific contacts
   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       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
   scorecmapdir Contact scores for cleaned protein chain contact 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    Generate ligand-binding signatures from a CON file
   sigscan      Generate hits (DHF file) from a signature search
   sigscanlig   Search ligand-signature library & write 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 (rranasin@rfcgr.mrc.ac.uk)
   Jon Ison (jison@rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, 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
