Translate nucleic acid sequences emboss transeq -sequence $input1 -outseq $out_file1 -frame $frame -table $table -regions "$regions" -trim $trim -clean $clean -alternative $alternative -osformat2 $out_format1 -auto Sequences Frame(s) to translate Frame 1 Frame 2 Frame 3 Forward three frames Frame -1 Frame -2 Frame -3 Reverse three frames All six frames 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 Regions to translate Remove all 'X' and '*' characters from the right end of the translation No Yes Change all STOP codon positions from the '*' character to 'X' No Yes Define frame '-1' as using the set of codons starting with the last codon of the sequence No Yes 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) GFF (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/transeq.html