Show features of a sequence emboss showfeat -sequence $input1 -outfile $out_file1 -matchsource "$matchsource" -matchtype "$matchtype" -matchtag "$matchtag" -matchvalue "$matchvalue" -sort $sort -annotation "$annotation" -id $id -description "$description" -scale "$scale" -width "$width" -collapse $collapse -forward $forward -reverse $reverse -unknown $unknown -strand $strand -source $source -position $position -type $type -tags $tags -values $values -stricttags $stricttags -html $html_out1 -auto Sequences Format output as an HTML table No Yes Feature source to match Feature type to match Feature tags to match Tag values to match Sort by Start position Source Type No sorting done Join coding regions together Regions to annotate by marking Display the ID name of the sequence Yes No Display the description of the sequence Yes No Display the scale line Yes No Screen width Collapse features No Yes Display forward sense features Yes No Display reverse sense features Yes No Display unknown sense features Yes No Display the strand of the features No Yes Display the source of the features No Yes SDisplay the start and end position of the features No Yes Display the type of the features Yes No Display the tags and values of the features No Yes Display the tag values of the features Yes No Display only those tag/value pairs in a feature that match the specified tag and value No Yes You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/showfeat.html