Finds neighbouring pairs of features in sequences emboss twofeat -sequence $input1 -outfile $out_file1 -atype "$atype" -btype "$btype" -minrange "$minrange" -maxrange "$maxrange" -asource "$asource" -asense $asense -aminscore "$aminscore" -amaxscore "$amaxscore" -atag "$atag" -avalue "$avalue" -bsource "$bsource" -bsense "$bsense" -bminscore "$bminscore" -bmaxscore "$bmaxscore" -btag "$btag" -bvalue "$bvalue" -overlap $overlap -rangetype $rangetype -sense $sense -order $order -twoout $twoout -typeout "$typeout" -rformat2 $out_format1 -auto Sequences Feature type you wish to allow. Feature 1 Feature type you wish to allow. Feature 2 Minimun range Maximum range Feature source 1 Feature sense 1 Any sense Forward sense Reverse sense Feature 1 minimum score Feature1 maxiumum score Feature 1 tag Tag 1 value Feature 2 source Feature 2 sense Any sense Forward sense Reverse sense Feature 2 miniumum score Feature 2 maximum score Feature 2 tag Feature 2 tag value opverlaps allowed Any Overlap required but not within No overlaps are allowed Overlap required but not within A must be all within B B must be all within A How to determine range From nearest ends From left ends From right ends From furthest ends Required sense Any sense Same sense Opposite sense Required order of the two features Any Feature A then feature B Feature B then feature A Write out the two features themselves No Yes New feature type Output Report File Format Table EMBL GENBANK GFF PIR SwissProt DbMotif Diffseq Excel (tab delimited) FeatTable Motif Regions SeqTable SRS Simple SRS TagSeq You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/twofeat.html