application: trimseq [ documentation: "Remove unwanted characters from start and end of sequence(s)" groups: "Edit" ] section: input [ information: "Input section" type: "page" ] seqall: sequence [ parameter: "Y" type: "gapany" ] endsection: input section: additional [ information: "Additional section" type: "page" ] integer: window [ additional: "Y" default: "1" information: "Window size" help: "This determines the size of the region that is considered when deciding whether the percentage of ambiguity is greater than the threshold. A value of 5 means that a region of 5 letters in the sequence is shifted along the sequence from the ends and trimming is done only if there is a greater or equal percentage of ambiguity than the threshold percentage." ] float: percent [ additional: "Y" default: "100.0" information: "Percent threshold of ambiguity in window" help: "This is the threshold of the percentage ambiguity in the window required in order to trim a sequence." ] boolean: strict [ additional: "Y" default: "N" information: "Trim off all ambiguity codes, not just N or X" help: "In nucleic sequences, trim off not only N's and X's, but also the nucleotide IUPAC ambiguity codes M, R, W, S, Y, K, V, H, D and B. In protein sequences, trim off not only X's but also B and Z." ] boolean: star [ additional: "Y" default: "N" information: "Trim off asterisks" help: "In protein sequences, trim off not only X's, but also the *'s" ] endsection: additional section: advanced [ information: "Advanced section" type: "page" ] boolean: left [ default: "Y" information: "Trim at the start" ] boolean: right [ default: "Y" information: "Trim at the end" ] endsection: advanced section: output [ information: "Output section" type: "page" ] seqoutall: outseq [ parameter: "Y" ] endsection: output