]> Translate nucleic acid sequences (EMBOSS) nucleic:translation http://bioweb.pasteur.fr/docs/EMBOSS/transeq.html transeq &emboss_init; input Input section sequence sequence -- nucleotide [sequences] (-sequence) perl " -sequence=$value -sformat=fasta" 1 nucleotide 8 seqsfile perl 1 advanced Advanced section frame Frame(s) to translate -- Translation frames [select values] (-frame) 1 1 2 2 3 3 F Forward three frames -1 -1 -2 -2 -3 -3 R Reverse three frames 6 All six frames , 1 perl " -frame=$value" 2 table Code to use -- Genetic codes (-table) 0 Standard 1 Standard (with alternative initiation codons) 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 16 Chlorophycean Mitochondrial 21 Trematode Mitochondrial 22 Scenedesmus obliquus 23 Thraustochytrium Mitochondrial 0 perl " -table=$value" 3 regions Regions to translate (eg: 4-57,78-94) (-regions) acd $sequence.begin-$sequence.end perl (defined $value && $value != $vdef)? " -regions=$value" : "" 4 Regions to translate. <BR> If this is left blank, then the complete sequence is translated. <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 <BR> Note: you should not try to use this option with any other frame than the default, -frame=1 trim Trim trailing X's and *'s (-trim) 0 perl ($value)? " -trim" : "" 5 This removes all 'X' and '*' characters from the right end of the translation. The trimming process starts at the end and continues until the next character is not a 'X' or a '*' clean Change all *'s to X's (-clean) 0 perl ($value)? " -clean" : "" 6 This changes all STOP codon positions from the '*' character to 'X' (an unknown residue). This is useful because some programs will not accept protein sequences with '*' characters in them. alternative Define frame '-1' as starting in the last codon (-alternative) 0 perl ($value)? " -alternative" : "" 7 The default definition of frame '-1' is the reverse-complement of the set of codons used in frame 1. (Frame -2 is the set of codons used by frame 2, similarly frames -3 and 3). This is a common standard, used by the Staden package and other programs. If you prefer to define frame '-1' as using the set of codons starting with the last codon of the sequence, then set this to be true. output Output section outseq outseq -- stopprotein (-outseq) outseq.out perl " -outseq=$value" 8 seqsfile perl 1 outseq_sformat Output format for: outseq -- stopprotein fasta fasta gcg gcg phylip phylip embl embl swiss swiss ncbi ncbi nbrf nbrf genbank genbank ig ig codata codata strider strider acedb acedb staden staden text text fitch fitch msf msf clustal clustal phylip phylip phylip3 phylip3 asn1 asn1 fasta perl " -osformat=$value" 9 auto perl " -auto -stdout" 10