Search LGIC databases Le Novere, Changeux Nicolas LE NOVERE and Jean-Pierre CHANGEUX (1999). The Ligand-Gated Ion Channel database. Nucleic Acid Research, 27 : 340-342 http://www.pasteur.fr/recherche/banques/LGIC/LGIC.html lgicsearch lgicsearch Fasta program perl $value fasta_t 0 fasta_t fasta: protein or DNA query vs similar db (FASTA release 3.0) tfasta_t tfasta: protein query vs translated DNA db (rel 3.0) query Query sequence File perl " $value" 2 8 seqtype Is it a DNA or protein sequence perl (($lgicsearch =~ /^fasta/ && $value eq "DNA") || $lgicsearch =~ /^fast(x|y)/)? " -n":"" 1 DNA DNA protein protein tfasta, tfastx and tfasty take a protein sequence perl $lgicsearch =~ /^tfast/ && $seqtype eq "DNA" protein_db Protein Database perl " /local/databases/fasta/$value" allpep 3 lgicallpep lgicallpep: all super-families lgicachpep lgicachpep: acetylcholine super-family subunits lgicglupep lgicglupep: glutamate excitatory super-family lgicatppep lgicatppep: ATP super-family perl ($seqtype eq "protein" && $lgicsearch =~ /^fasta/) nucleotid_db Nucleotid Database perl " /local/databases/fasta/$value" allnuc 3 lgicallnuc lgicallnuc: all super-families lgicachnuc lgicachnuc: acetylcholine super-family subunits lgicglunuc lgicglunuc: glutamate excitatory super-family lgicatpnuc lgicatpnuc: ATP super-family perl ($seqtype eq "DNA" && $lgicsearch =~ /^fasta/ ) || $lgicsearch =~ /^tfast/ ktup perl (defined $value)? " 1":"" 4 threeframe (tfasta only) only the three forward frames are searched perl ($value)? " -3":"" perl ($lgicsearch =~ /^tfasta/) 1 tmp_outfile lgicsearch.txt mview_input perl 1 txtoutput perl " > lgicsearch.txt" 7 lgicdbf2h perl " && lgicdbf2h < lgicsearch.txt > lgicsearch.html " 100 html_outfile lgicsearch.html