4.2 search protein sequences for similarity to AACC patterns R. Smith & T. Smit Smith, Randall F. and Temple F. Smith (1990). Automatic generation of diagnostic sequence patterns from sets of related protein sequences. Proc. Natl. Acad. Sci. USA 87:118-122. motifs protein:motifs plsearch plsearch perl "readseq -p -f1 < $protein | IG-to-tbl > tmp; cp tmp $protein; plsearch < params " 0 type perl "1\\n" 1 params no_detach perl "no\\n" 5 params protein Protein sequence File perl `basename $value` 2 params outfile Results file perl ($value)? "$value\\n" : "plsearch.res\\n" plsearch.res 3 params max_alignements Maximum number of alignments perl (defined $value && $value != $vdef)? "$value\\n":"$vdef\\n" 20 4 This value sets the maximum, however all matches with SDAM values greater than 4.0 will be displayed regardless of the value specified here. params params params