Predicts protein secondary structure emboss garnier -sequence $input1 -outfile $out_file1 -idc $idc -rformat2 $out_format1 -auto Sequences In their paper, GOR mention that if you know something about the secondary structure content of the protein you are analyzing, you can do better in prediction. 'idc' is an index into a set of arrays, dharr[] and dsarr[], which provide 'decision constants' (dch, dcs), which are offsets that are applied to the weights for the helix and sheet (extend) terms. So, idc=0 says don't use the decision constant offsets, and idc=1 to 6 indicates that various combinations of dch,dcs offsets should be used idc 0 idc 1 idc 2 idc 3 idc 4 idc 5 idc 6 Output Report File Format TagSeq EMBL GENBANK GFF PIR SwissProt DbMotif Diffseq Excel (tab delimited) FeatTable Motif Regions SeqTable SRS Simple SRS Table

You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/garnier.html