]> SIXPACK Display a DNA sequence with 6-frame translation and ORFs (EMBOSS) display nucleic:gene finding nucleic:translation http://bioweb.pasteur.fr/docs/EMBOSS/sixpack.html sixpack &emboss_init; input Input section sequence sequence -- DNA [single sequence] (-sequence) perl " -sequence=$value -sformat=fasta" 1 dna 8 seqfile perl 1 advanced Advanced section table Code to use -- Genetic codes (-table) 0 1 2 3 4 5 6 9 10 11 12 13 14 15 16 21 22 23 0 perl " -table=$value" 2 Genetics code used for the translation firstorf ORF at the beginning of the sequence (-firstorf) 1 perl ($value)? "" : " -nofirstorf" 3 Count the beginning of a sequence as a possible ORF, even if it's inferior to the minimal ORF size. lastorf ORF at the end of the sequence (-lastorf) 1 perl ($value)? "" : " -nolastorf" 4 Count the end of a sequence as a possible ORF, even if it's not finishing with a STOP, or inferior to the minimal ORF size. mstart ORF start with an M (-mstart) 0 perl ($value)? " -mstart" : "" 5 Displays only ORFs starting with an M. output Output section outfile outfile (-outfile) outfile.out perl " -outfile=$value" 6 outseq outseq -- stopprotein (-outseq) perl ($value)? " -outseq=$value" : "" 7 ORF sequence output seqsfile perl 1 outseq_sformat Output format for: outseq -- stopprotein fasta gcg phylip embl swiss ncbi nbrf genbank ig codata strider acedb staden text fitch msf clustal phylip phylip3 asn1 fasta perl " -osformat=$value" 8 reverse Display translation of reverse sense (-reverse) 1 perl ($value)? "" : " -noreverse" 9 Display also the translation of the DNA sequence in the 3 reverse frames orfminsize Minimum size of ORFs (-orfminsize) 1 perl (defined $value && $value != $vdef)? " -orfminsize=$value" : "" 10 Minimum size of Open Reading Frames (ORFs) to display in the translations. 1 uppercase Regions to put in uppercase (eg: 4-57,78-94) (-uppercase) perl ($value)? " -uppercase=$value" : "" 11 Regions to put in uppercase. <BR> If this is left blank, then the sequence case is left alone. <BR> A set of regions is specified by a set of pairs of positions. <BR> The positions are integers. <BR> They are separated by any non-digit, non-alpha character. <BR> Examples of region specifications are: <BR> 24-45, 56-78 <BR> 1:45, 67=99;765..888 <BR> 1,5,8,10,23,45,57,99 highlight Regions to colour in HTML (eg: 4-57 red 78-94 green) (-highlight) perl ($value)? " -highlight=$value" : "" 12 Regions to colour if formatting for HTML. <BR> If this is left blank, then the sequence is left alone. <BR> A set of regions is specified by a set of pairs of positions. <BR> The positions are integers. <BR> They are followed by any valid HTML font colour. <BR> Examples of region specifications are: <BR> 24-45 blue 56-78 orange <BR> 1-100 green 120-156 red <BR> A file of ranges to colour (one range per line) can be specifed as '\@filename'. number Number the sequences (-number) 1 perl ($value)? "" : " -nonumber" 13 Number the sequence at the beginning and the end of each line. width Width of sequence to display (-width) 60 perl (defined $value && $value != $vdef)? " -width=$value" : "" 14 Number of nucleotides displayed on each line 1 length Line length of page (0 for indefinite) (-length) 0 perl (defined $value && $value != $vdef)? " -length=$value" : "" 15 margin Margin around sequence for numbering. (-margin) 10 perl (defined $value && $value != $vdef)? " -margin=$value" : "" 16 name Display sequence ID (-name) 1 perl ($value)? "" : " -noname" 17 Set this to be false if you do not wish to display the ID name of the sequence. description Display description (-description) 1 perl ($value)? "" : " -nodescription" 18 Set this to be false if you do not wish to display the description of the sequence. offset Offset to start numbering the sequence from (-offset) 1 perl (defined $value && $value != $vdef)? " -offset=$value" : "" 19 Number from which you want the DNA sequence to be numbered. html Use HTML formatting (-html) 0 perl ($value)? " -html" : "" 20 auto perl " -auto -stdout" 21