Protein Structure

[Dr J.C. Ison]

 Major new revision of protein structure applications - w/o full
documentation.

 Gary - the documentation that can be used is the one-line summaries
given
 at the end of this msg.   Full documentation plus user-guide to follow
soon.

 New applications have been cvs add'ed:
      pdbparse.c / acd
      scopseqs.c / acd
      scopnr.c / acd
      seqsearch.c / acd
      seqwords.c / acd
      seqalign.c / acd
      hetparse.c / acd
      scopreso.c / acd
      scoprep.c / acd
      profgen.c / acd
      funky.c / acd
      hmmgen.c / acd

 Some applications have been cvs delete'd:
      scope.c / acd
      nrscope.c / acd
      psiblasts.c / acd
      swissparse.c / acd
      alignwrap.c / acd
      dichet.c / acd

 The deleted applications have been replaced as follows:
      coordenew  --> pdbparse (coordnew was deleted a while back)
      scope --> scopparse
      nrscope --> scopnr
      psiblasts --> seqsearch
      swissparse --> seqwords
      alignwrap  --> seqalign

 New versions of code have been cvs commit'ed:
      pdbparse.c / acd
      domainer.c / acd
      contacts.c / acd
      interface.c / acd
      pdbtosp.c / acd
      scopparse.c / acd
      scopreso.c / acd
      scopseqs.c / acd
      scopnr.c / acd
      scoprep.c / acd
      scopalign.c / acd
      seqsearch.c / acd
      seqwords.c / acd
      seqsort.c / acd
      seqnr.c / acd
      seqalign.c / acd
      siggen.c / acd
      sigscan.c / acd
      sigplot.c / acd
      hetparse.c / acd
      profgen.c / acd
      funky.c / acd
      hmmgen.c / acd
 Plus
      ajxyz.c / ajxyz.h

 Short summaries of the applications are as follows:
      pdbparse - Parses pdb files and writes cleaned-up protein
                          coordinate files.
      domainer - Reads protein coordinate files and writes
                          domains coordinate files.
      contacts -   Reads coordinate files and writes files of
                           intra-chain residue-residue contact data.
      interface-    Reads coordinate files and writes files of
                           inter-chain residue-residue contact data.
      pdbtosp  -   Convert raw swissprot:pdb equivalence file to
                           embl-like format.
      scopparse- Converts raw scop classification files to a
                           file in embl-like format.
      scopreso -  Removes low resolution domains from a scop
                          classification file.
      scopseqs - Adds pdb and swissprot sequence records to a
                          scop classification file.
      scopnr   -    Removes redundant domains from a scop
                          classification file.
      scoprep  -   Reorder scop classificaiton file so that the
                           representative structure of each family is
                          given first.
      scopalign-  Generate alignments for families in a scop
                          classification file by using STAMP.
      seqsearch- Generate files of hits for families in a scop
                          classification file by using PSI-BLAST with
                          seed alignments.
      seqwords - Generate files of hits for scop families by
                          searching swissprot with keywords.
      seqsort  -   Reads multiple files of hits and writes a
                           non-ambiguous file of hits (scop families
file)
                           plus a validation file.
      seqnr    -    Removes redundant hits from a scop families file.
      seqalign -  Generate extended alignments for families in
                          a scop families file by using CLUSTALW with
seed
                          alignments.
      siggen   -   Generates a sparse protein signature from an
                          alignment and residue contact data.
      sigscan  -   Scans a signature against swissprot and writes
                          a signature hits files.
      sigplot  -    Reads a signature hits file and validation file
                          and generates gnuplot data files of signature
                          performance.
      profgen  -   Generates various profiles for each alignment
                          in a directory.
      hmmgen   - Generates a hidden Markov model for each alignment
                           in a directory.
      hetparse -  Converts raw dictionary of heterogen groups to
                           a file in embl-like format.
      funky    -     Reads clean coordinate files and writes file
                           of protein-heterogen contact data.



J.

--
Jon C. Ison, PhD
Bioinformatics Applications Group
UK MRC Human Genome Mapping Project Resource Centre
Hinxton, Cambridge, CB10 1SB, UK
E-mail : jison at hgmp.mrc.ac.uk