Finds and extracts open reading frames (ORFs) emboss getorf -sequence $input1 -outseq $out_file1 -table $table -minsize $minsize -maxsize $maxsize -find $find -methionine $methionine -circular $circular -reverse $reverse -flanking $flanking -osformat2 $out_format1 -auto Sequences Code to use Standard Standard (with alternative initiation codons) Vertebrate Mitochondrial Yeast Mitochondrial Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma Invertebrate Mitochondrial Ciliate Macronuclear and Dasycladacean Echinoderm Mitochondrial Euplotid Nuclear Bacterial Alternative Yeast Nuclear Ascidian Mitochondrial Flatworm Mitochondrial Blepharisma Macronuclear Chlorophycean Mitochondrial Trematode Mitochondrial Scenedesmus obliquus Thraustochytrium Mitochondrial Minimum nucleotide size of ORF to report Maximum nucleotide size of ORF to report What to output Translation of regions between STOP codons Translation of regions between START and STOP codons Nucleic sequences between STOP codons Nucleic sequences between START and STOP codons Nucleotides flanking START codons Nucleotides flanking initial STOP codons Nucleotides flanking ending STOP codons All START codons to code for Methionine Yes No Circular sequence No Yes Find ORFs in the reverse complement Yes No Number of flanking nucleotides to output Output Sequence File Format FASTA (m) ACeDB (m) ASN.1 (m) Clustal (m) CODATA (m) EMBL (m) Fitch (m) Wisconsin Package GCG 9.x and 10.x (s) GENBANK (m) Hennig86 (m) Intelligenetics (m) Jackknifer (m) Jackknifernon (m) Mega (m) Meganon (m) Wisconsin Package GCG's MSF (m) NBRF (PIR) (m) NCBI style FASTA (m) Nexus/PAUP (m) Nexusnon/PAUPnon (m) PHYLIP interleaved (m) PHYLIP non-interleaved (m) SELEX (m) Staden (s) DNA strider (m) SwisProt entry (m) Plain sequence (s) Treecon (m)

.. class:: warningmark The input dataset needs to be sequences. ----- You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/getorf.html