]> Trim ambiguous bits off the ends of sequences (EMBOSS) edit http://bioweb.pasteur.fr/docs/EMBOSS/trimseq.html trimseq &emboss_init; input Input section sequence sequence -- gapany [sequences] (-sequence) perl " -sequence=$value -sformat=fasta" 1 gapany 8 seqsfile perl 1 advanced Advanced section window Window size (-window) 1 perl (defined $value && $value != $vdef)? " -window=$value" : "" 2 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. percent Percent threshold of ambiguity in window (-percent) 100.0 perl (defined $value && $value != $vdef)? " -percent=$value" : "" 3 This is the threshold of the percentage ambiguity in the window required in order to trim a sequence. strict Trim off all ambiguity codes, not just N or X (-strict) 0 perl ($value)? " -strict" : "" 4 In nucleic sequences, trim off not only N's and X's, but also the nucleotide IUPAC ambiguity codes M, R, W, S, Y, K, V, H, D and B. In protein sequences, trim off not only X's but also B and Z. star Trim off asterisks (-star) 0 perl ($value)? " -star" : "" 5 In protein sequences, trim off not only X's, but also the *'s left Trim at the start (-left) 1 perl ($value)? "" : " -noleft" 6 right Trim at the end (-right) 1 perl ($value)? "" : " -noright" 7 output Output section outseq outseq (-outseq) outseq.out perl " -outseq=$value" 8 seqsfile perl 1 outseq_sformat Output format for: outseq fasta fasta gcg gcg phylip phylip embl embl swiss swiss ncbi ncbi nbrf nbrf genbank genbank ig ig codata codata strider strider acedb acedb staden staden text text fitch fitch msf msf clustal clustal phylip phylip phylip3 phylip3 asn1 asn1 fasta perl " -osformat=$value" 9 auto perl " -auto -stdout" 10