NAME

       afetch - retrieve an alignment from an alignment database

SYNOPSIS

       afetch [options] alignmentdb key

       afetch --index alignmentdb

DESCRIPTION

       afetch retrieves the alignment named key from an alignment database in file alignmentdb.

       alignmentdb  is  a  "multiple  multiple  alignment"  file  in Stockholm (e.g. native Pfam)
       format.

       key is either the name (ID) of the alignment, or its accession number (AC).

       The alignmentdb file should first  be  SSI  indexed  with  afetch  --index  for  efficient
       retrieval.  An  SSI  index  is  not  required,  but alignment retrieval without one may be
       painfully slow.

OPTIONS

       -h     Print brief help; includes version number and summary  of  all  options,  including
              expert options.

EXPERT OPTIONS

       --index
              Instead  of  retrieving  a  key,  the  special  command  afetch --index alignmentdb
              produces an SSI index of the names and accessions of the  alignments  in  the  file
              alignmentdb.  This should be run once on the alignmentdb file to prepare it for all
              future afetch's.

SEE ALSO

       alistat(1), compalign(1), compstruct(1), revcomp(1), seqsplit(1),  seqstat(1),  sfetch(1),
       shuffle(1), sindex(1), sreformat(1), stranslate(1), weight(1).

AUTHOR

       Biosquid  and  its  documentation  are  Copyright (C) 1992-2003 HHMI/Washington University
       School of Medicine Freely distributed under the  GNU  General  Public  License  (GPL)  See
       COPYING in the source code distribution for more details, or contact me.

       Sean Eddy
       HHMI/Department of Genetics
       Washington University School of Medicine
       4444 Forest Park Blvd., Box 8510
       St Louis, MO 63108 USA
       Phone: 1-314-362-7666
       FAX  : 1-314-362-2157
       Email: eddy@genetics.wustl.edu