Extract features from a sequence emboss extractfeat -sequence $input1 -outseq $out_file1 -before $before -after $after -source "$source" -type "$type" -sense $sense -minscore $minscore -maxscore $maxscore -tag "$tag" -value "$value" -join $join -featinname $featinname -describe "$describe" -osformat2 $out_format1 -auto Sequences Number of bases or residues before the feature to include in the extracted sequence Number of bases or residues after the feature to include in the extracted sequence Feature source Feature type Feature sense Any sense Forward sense Reverse sense Minimum score Maximum score Feature tags Tag values Join features No Yes Put feature type in sequence name No Yes Specify one or more tag names that should be added to the output sequence Description text 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) You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/extractfeat.html