]> Information on a multiple sequence alignment (EMBOSS) alignment:multiple information http://bioweb.pasteur.fr/docs/EMBOSS/infoalign.html infoalign &emboss_init; input Input section sequence sequence -- gapany [set of sequences] (-sequence) perl " -sequence=$value -sformat=fasta" 1 The sequence alignment to be displayed. gapany 8 seqsfile perl 1 advanced Advanced section refseq The number or the name of the reference sequence (-refseq) 0 perl ($value && $value ne $vdef)? " -refseq=$value" : "" 2 If you give the number in the alignment or the name of a sequence, it will be taken to be the reference sequence. The reference sequence is the one against which all the other sequences are compared. If this is set to 0 then the consensus sequence will be used as the reference sequence. By default the consensus sequence is used as the reference sequence. matrix Similarity scoring Matrix file (-matrix) 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 ($value)? " -matrix=$value" : "" 3 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 % for consensus (-plurality) 50.0 perl (defined $value && $value != $vdef)? " -plurality=$value" : "" 4 Set a cut-off for the % of positive scoring matches below which there is no consensus. The default plurality is taken as 50% of the total weight of all the sequences in the alignment. 0.0 100.0 identity Required % of identities at a position fro consensus (-identity) 0.0 perl (defined $value && $value != $vdef)? " -identity=$value" : "" 5 Provides the facility of setting the required number of identities at a position for it to give a consensus. Therefore, if this is set to 100% only columns of identities contribute to the consensus. 0.0 100.0 output Output section outfile outfile (-outfile) outfile.out perl " -outfile=$value" 6 If you enter the name of a file here then this program will write the sequence details into that file. html Format output as an HTML table (-html) 0 perl ($value)? " -html" : "" 7 only Display the specified columns (-only) 0 perl ($value)? " -only" : "" 8 This is a way of shortening the command line if you only want a few things to be displayed. Instead of specifying: <BR> '-nohead -nousa -noname -noalign -nogaps -nogapcount -nosimcount -noidcount -nodiffcount' <BR> to get only the sequence length output, you can specify <BR> '-only -seqlength' heading Display column headings (-heading) acd @(!$(only)) perl ($value)? " -heading" : "" 9 usa Display the USA of the sequence (-usa) acd @(!$(only)) perl ($value)? " -usa" : "" 10 name Display 'name' column (-name) acd @(!$(only)) perl ($value)? " -name" : "" 11 seqlength Display 'seqlength' column (-seqlength) acd @(!$(only)) perl ($value)? " -seqlength" : "" 12 alignlength Display 'alignlength' column (-alignlength) acd @(!$(only)) perl ($value)? " -alignlength" : "" 13 gaps Display number of gaps (-gaps) acd @(!$(only)) perl ($value)? " -gaps" : "" 14 gapcount Display number of gap positions (-gapcount) acd @(!$(only)) perl ($value)? " -gapcount" : "" 15 idcount Display number of identical positions (-idcount) acd @(!$(only)) perl ($value)? " -idcount" : "" 16 simcount Display number of similar positions (-simcount) acd @(!$(only)) perl ($value)? " -simcount" : "" 17 diffcount Display number of different positions (-diffcount) acd @(!$(only)) perl ($value)? " -diffcount" : "" 18 change Display % number of changed positions (-change) acd @(!$(only)) perl ($value)? " -change" : "" 19 description Display 'description' column (-description) acd @(!$(only)) perl ($value)? " -description" : "" 20 auto perl " -auto -stdout" 21