Search Coding Regions F. Chauveau nucleic:translation gene finding cds cds seqlab cds perl "cds" 0 seq Sequence File perl " $value" 10 search Search parameters minaa Minimum number of amino acids in CDS perl ($value)? " -l $value" : "" 1 frame Frame perl ($value)? " -f $value" : "" 1 1 1 2 2 3 3 -1 1 (opposite strand) -2 2 (opposite strand) -3 3 (opposite strand) starts START codons (separated by commas) perl ($value && ($value !~ /,/ || $value =~ s/,/ /g) )? " -c \\"$value\\" " : "" 1 maxf longest CDS in each frame perl ($value)? " -m":"" 0 1 max longest CDS perl ($value)? " -M":"" 0 1 all all CDS, including CDS inside CDS perl ($value)? " -a":"" 0 1 output Output parameters nucl nucleotids output perl ($value)? " -n":"" 0 1 print_adn Print ADN as well as Amino-acids perl ($print_adn || defined $left_adn)? " -v $left_adn" : "" 0 1 left_adn How many base pairs on the left (if print ADN) perl "" 1 print_frame print frame before search perl ($value)? " -s":"" 0 1 print_pos print only position(s) perl ($value)? " -p":"" 0 1 xml XML output (-x) perl ($value)? " -x":"" 0 1 xmldtdcopy perl "; cp /local/gensoft/lib/pasteur/cds.dtd ." 100 perl $xml xmldtd perl $xml cds.dtd others Other parameters end_stop CDS ends at STOP perl ($value)? " -e":"" 0 1 genetic Genetic Code perl ($value && $value ne $vdef)? " -g $value" : "" 1 1 1 Standard 2 Vertebrate Mitochondrial 3 Yeast Mitochondrial 4 Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma 5 Invertebrate Mitochondrial 6 Ciliate Macronuclear and Dasycladacean 9 Echinoderm Mitochondrial 10 Euplotid Nuclear 11 Bacterial 12 Alternative Yeast Nuclear 13 Ascidian Mitochondrial 14 Flatworm Mitochondrial 15 Blepharisma Macronuclear