Protein pattern search after translation emboss fuzztran -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -frame $frame -table $table -rformat2 $out_format1 -auto Sequences Search pattern Number of mismatches 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 Output Report File Format Table EMBL GENBANK GFF PIR SwissProt DbMotif Diffseq Excel (tab delimited) FeatTable Motif Regions SeqTable SRS Simple SRS TagSeq

.. 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/fuzztran.html