]> Finds and extracts open reading frames (ORFs) (EMBOSS) nucleic:gene finding http://bioweb.pasteur.fr/docs/EMBOSS/getorf.html getorf &emboss_init; input Input section sequence sequence -- DNA [sequences] (-sequence) perl " -sequence=$value -sformat=fasta" 1 dna 8 seqsfile perl 1 advanced Advanced section table Code to use -- Genetic codes (-table) 0 Standard 1 Standard (with alternative initiation codons) 2 Vertebrate Mitochondrial 3 Yeast Mitochondrial 4 Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma 5 Invertebrate Mitochondrial 6 Ciliate Macronuclear and Dasycladacean 9 Echinoderm Mitochondrial 10 Euplotid Nuclear 11 Bacterial 12 Alternative Yeast Nuclear 13 Ascidian Mitochondrial 14 Flatworm Mitochondrial 15 Blepharisma Macronuclear 16 Chlorophycean Mitochondrial 21 Trematode Mitochondrial 22 Scenedesmus obliquus 23 Thraustochytrium Mitochondrial 0 perl " -table=$value" 2 minsize Minimum nucleotide size of ORF to report (-minsize) 30 perl (defined $value && $value != $vdef)? " -minsize=$value" : "" 3 maxsize Maximum nucleotide size of ORF to report (-maxsize) 1000000 perl (defined $value && $value != $vdef)? " -maxsize=$value" : "" 4 find Type of output -- Type of sequence to output (-find) 0 Translation of regions between STOP codons 1 Translation of regions between START and STOP codons 2 Nucleic sequences between STOP codons 3 Nucleic sequences between START and STOP codons 4 Nucleotides flanking START codons 5 Nucleotides flanking initial STOP codons 6 Nucleotides flanking ending STOP codons 0 perl " -find=$value" 5 This is a small menu of possible output options. The first four options are to select either the protein translation or the original nucleic acid sequence of the open reading frame. There are two possible definitions of an open reading frame: it can either be a region that is free of STOP codons or a region that begins with a START codon and ends with a STOP codon. The last three options are probably only of interest to people who wish to investigate the statistical properties of the regions around potential START or STOP codons. The last option assumes that ORF lengths are calculated between two STOP codons. methionine Change initial START codons to Methionine (-methionine) 1 perl ($value)? "" : " -nomethionine" 6 START codons at the beginning of protein products will usually code for Methionine, despite what the codon will code for when it is internal to a protein. This qualifier sets all such START codons to code for Methionine by default. circular Is the sequence circular (-circular) 0 perl ($value)? " -circular" : "" 7 reverse Find ORFs in the reverse sequence (-reverse) 1 perl ($value)? "" : " -noreverse" 8 Set this to be false if you do not wish to find ORFs in the reverse complement of the sequence. flanking Number of flanking nucleotides to report (-flanking) 100 perl (defined $value && $value != $vdef)? " -flanking=$value" : "" 9 If you have chosen one of the options of the type of sequence to find that gives the flanking sequence around a STOP or START codon, this allows you to set the number of nucleotides either side of that codon to output. If the region of flanking nucleotides crosses the start or end of the sequence, no output is given for this codon. output Output section outseq outseq -- stopprotein (-outseq) outseq.out perl " -outseq=$value" 10 seqsfile perl 1 outseq_sformat Output format for: outseq -- stopprotein fasta fasta gcg gcg phylip phylip embl embl swiss swiss ncbi ncbi nbrf nbrf genbank genbank ig ig codata codata strider strider acedb acedb staden staden text text fitch fitch msf msf clustal clustal phylip phylip phylip3 phylip3 asn1 asn1 fasta perl " -osformat=$value" 11 auto perl " -auto -stdout" 12