]> Needleman-Wunsch global alignment. (EMBOSS) alignment:global http://bioweb.pasteur.fr/docs/EMBOSS/needle.html needle &emboss_init; input Input section asequence asequence -- any [single sequence] (-asequence) perl " -asequence=$value -sformat=fasta" 1 any 8 seqfile perl 1 bsequence bsequence [sequences] (-bsequence) perl " -bsequence=$value -sformat=fasta" 2 acd @($(acdprotein) ? stopprotein : nucleotide) 8 seqsfile perl 1 required Required section gapopen Gap opening penalty (-gapopen) acd @($(acdprotein)? 10.0 : 10.0 ) perl " -gapopen=$value" 3 The gap open penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences. Allowed values: Floating point number from 1.0 to 100.0 1. 100. gapextend Gap extension penalty (-gapextend) acd @($(acdprotein)? 0.5 : 0.5 ) perl " -gapextend=$value" 4 The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. Allowed values: Floating point number from 0.0 to 10.0 0.0 10. advanced Advanced section datafile Matrix file (-datafile) EPAM60 EPAM60 EPAM290 EPAM290 EPAM470 EPAM470 EPAM110 EPAM110 EBLOSUM50 EBLOSUM50 EPAM220 EPAM220 EBLOSUM62-12 EBLOSUM62-12 EPAM400 EPAM400 EPAM150 EPAM150 EPAM330 EPAM330 EBLOSUM55 EBLOSUM55 EPAM30 EPAM30 EPAM260 EPAM260 EBLOSUM90 EBLOSUM90 EPAM440 EPAM440 EPAM190 EPAM190 EPAM370 EPAM370 EPAM70 EPAM70 EPAM480 EPAM480 EPAM120 EPAM120 EDNAMAT EDNAMAT EPAM300 EPAM300 EBLOSUM60 EBLOSUM60 EPAM230 EPAM230 EBLOSUM62 EBLOSUM62 EPAM410 EPAM410 EPAM160 EPAM160 EPAM340 EPAM340 EBLOSUM65 EBLOSUM65 EPAM40 EPAM40 EPAM270 EPAM270 EPAM450 EPAM450 EPAM380 EPAM380 EPAM80 EPAM80 EPAM490 EPAM490 EBLOSUM30 EBLOSUM30 EBLOSUMN EBLOSUMN EPAM200 EPAM200 EPAM130 EPAM130 EBLOSUM35 EBLOSUM35 EPAM310 EPAM310 EBLOSUM70 EBLOSUM70 EPAM10 EPAM10 EPAM240 EPAM240 EPAM420 EPAM420 EPAM170 EPAM170 EBLOSUM75 EBLOSUM75 EPAM350 EPAM350 EPAM280 EPAM280 EPAM50 EPAM50 EPAM460 EPAM460 EPAM390 EPAM390 EPAM90 EPAM90 EPAM100 EPAM100 EBLOSUM40 EBLOSUM40 EPAM210 EPAM210 EPAM140 EPAM140 EBLOSUM45 EBLOSUM45 EPAM320 EPAM320 EBLOSUM80 EBLOSUM80 EPAM500 EPAM500 EPAM20 EPAM20 EPAM250 EPAM250 EPAM430 EPAM430 EPAM180 EPAM180 EBLOSUM85 EBLOSUM85 EPAM360 EPAM360 perl ($value)? " -datafile=$value" : "" 5 This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation. output Output section brief Brief identity and similarity (-brief) 1 perl ($value)? "" : " -nobrief" 6 Brief identity and similarity outfile outfile (-outfile) outfile.align perl " -outfile=$value" 7 readseq_ok_alig perl $outfile_aformat ne "" outfile_aformat Alignment output format (-aformat) perl ($value)? " -aformat=$value" : "" default fasta fasta MSF MSF 7 auto perl " -auto -stdout" 8