Display a DNA sequence with 6-frame translation and ORFs emboss sixpack -sequence $input1 -outfile $ofile1 -outseq $ofile2 -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize -uppercase "$uppercase" -number $number -width "$width" -length "$length" -margin "$margin" -name $disp_name -description $description -offset "$offset" -html $html_out1 -osformat $out_format2 -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 Count the beginning of a sequence as a possible ORF Yes No Count the end of a sequence as a possible ORF Yes No Displays only ORFs starting with an M No Yes Display the translation of the DNA sequence in the 3 reverse frames Yes No Minimum size of Open Reading Frames (ORFs) to display in the translations Regions to put in uppercase Number the sequence at the beginning and the end of each line Yes No Number of nucleotides displayed on each line Line length of page Margin around sequence for numbering Display the ID name of the sequence Yes No Display the description of the sequence Yes No Number from which you want the DNA sequence to be numbered Format output as an HTML table 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/sixpack.html