]> Creates a consensus from multiple alignments (EMBOSS) alignment:consensus http://bioweb.pasteur.fr/docs/EMBOSS/cons.html cons &emboss_init; input Input section sequence sequence -- gapany [set of sequences] (-sequence) perl " -sequence=$value -sformat=fasta" 1 File containing a sequence alignment. gapany 8 seqsfile perl 1 advanced Advanced section datafile Scoring matrix (-datafile) EPAM60 EPAM60 EPAM290 EPAM290 EPAM470 EPAM470 EPAM110 EPAM110 EBLOSUM50 EBLOSUM50 EPAM220 EPAM220 EBLOSUM62-12 EBLOSUM62-12 EPAM400 EPAM400 EPAM150 EPAM150 EPAM330 EPAM330 EBLOSUM55 EBLOSUM55 EPAM30 EPAM30 EPAM260 EPAM260 EBLOSUM90 EBLOSUM90 EPAM440 EPAM440 EPAM190 EPAM190 EPAM370 EPAM370 EPAM70 EPAM70 EPAM480 EPAM480 EPAM120 EPAM120 EDNAMAT EDNAMAT EPAM300 EPAM300 EBLOSUM60 EBLOSUM60 EPAM230 EPAM230 EBLOSUM62 EBLOSUM62 EPAM410 EPAM410 EPAM160 EPAM160 EPAM340 EPAM340 EBLOSUM65 EBLOSUM65 EPAM40 EPAM40 EPAM270 EPAM270 EPAM450 EPAM450 EPAM380 EPAM380 EPAM80 EPAM80 EPAM490 EPAM490 EBLOSUM30 EBLOSUM30 EBLOSUMN EBLOSUMN EPAM200 EPAM200 EPAM130 EPAM130 EBLOSUM35 EBLOSUM35 EPAM310 EPAM310 EBLOSUM70 EBLOSUM70 EPAM10 EPAM10 EPAM240 EPAM240 EPAM420 EPAM420 EPAM170 EPAM170 EBLOSUM75 EBLOSUM75 EPAM350 EPAM350 EPAM280 EPAM280 EPAM50 EPAM50 EPAM460 EPAM460 EPAM390 EPAM390 EPAM90 EPAM90 EPAM100 EPAM100 EBLOSUM40 EBLOSUM40 EPAM210 EPAM210 EPAM140 EPAM140 EBLOSUM45 EBLOSUM45 EPAM320 EPAM320 EBLOSUM80 EBLOSUM80 EPAM500 EPAM500 EPAM20 EPAM20 EPAM250 EPAM250 EPAM430 EPAM430 EPAM180 EPAM180 EBLOSUM85 EBLOSUM85 EPAM360 EPAM360 perl ($value)? " -datafile=$value" : "" 2 This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation. plurality Plurality check value (-plurality) acd @( $(sequence.totweight) / 2) perl (defined $value && $value != $vdef)? " -plurality=$value" : "" 3 Set a cut-off for the number of positive matches below which there is no consensus. The default plurality is taken as half the total weight of all the sequences in the alignment. identity Required number of identities at a position (-identity) 0 perl (defined $value && $value != $vdef)? " -identity=$value" : "" 4 Provides the facility of setting the required number of identities at a site for it to give a consensus at that position. Therefore, if this is set to the number of sequences in the alignment only columns of identities contribute to the consensus. setcase Define a threshold above which the consensus is given in uppercase (-setcase) acd @( $(sequence.totweight) / 2) perl (defined $value && $value != $vdef)? " -setcase=$value" : "" 5 Sets the threshold for the positive matches above which the consensus is is upper-case and below which the consensus is in lower-case. output Output section outseq outseq (-outseq) outseq.out perl " -outseq=$value" 6 seqfile perl 1 outseq_sformat Output format for: outseq fasta fasta gcg gcg phylip phylip embl embl swiss swiss ncbi ncbi nbrf nbrf genbank genbank ig ig codata codata strider strider acedb acedb staden staden text text fitch fitch msf msf clustal clustal phylip phylip phylip3 phylip3 asn1 asn1 fasta perl " -osformat=$value" 7 name Name of the consensus sequence (-name) perl ($value)? " -name=$value" : "" 8 auto perl " -auto -stdout" 9