Trim ambiguous bits off the ends of sequences emboss trimseq -sequence $input1 -outseq $out_file1 -window "$window" -percent "$percent" -strict $strict -star $star -left $left -right $right -osformat2 $out_format1 -auto Sequences Window size Threshold of the percentage ambiguity Trim all ambiguity codes No Yes In protein sequences, trim off not only X's, but also the *'s No Yes Trim at the start Yes No Trim at the end Yes No Output Sequence File Format FASTA (m) ACeDB (m) ASN.1 (m) Clustal (m) CODATA (m) EMBL (m) Fitch (m) Wisconsin Package GCG 9.x and 10.x (s) GENBANK (m) GFF (m) Hennig86 (m) Intelligenetics (m) Jackknifer (m) Jackknifernon (m) Mega (m) Meganon (m) Wisconsin Package GCG's MSF (m) NBRF (PIR) (m) NCBI style FASTA (m) Nexus/PAUP (m) Nexusnon/PAUPnon (m) PHYLIP interleaved (m) PHYLIP non-interleaved (m) SELEX (m) Staden (s) DNA strider (m) SwisProt entry (m) Plain sequence (s) Treecon (m)

.. 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/trimseq.html