]> Align EST and genomic DNA sequences (EMBOSS) alignment:global http://bioweb.pasteur.fr/docs/EMBOSS/est2genome.html est2genome &emboss_init; input Input section est EST sequence(s) (-est) perl " -est=$value -sformat=fasta" 1 dna 8 seqsfile perl 1 genome Genomic sequence (-genome) perl " -genome=$value -sformat=fasta" 2 dna 8 seqfile perl 1 advanced Advanced section match Score for matching two bases (-match) 1 perl (defined $value && $value != $vdef)? " -match=$value" : "" 3 mismatch Cost for mismatching two bases (-mismatch) 1 perl (defined $value && $value != $vdef)? " -mismatch=$value" : "" 4 gappenalty Gap penalty (-gappenalty) 2 perl (defined $value && $value != $vdef)? " -gappenalty=$value" : "" 5 Cost for deleting a single base in either sequence, excluding introns intronpenalty Intron penalty (-intronpenalty) 40 perl (defined $value && $value != $vdef)? " -intronpenalty=$value" : "" 6 Cost for an intron, independent of length. splicepenalty Splice site penalty (-splicepenalty) 20 perl (defined $value && $value != $vdef)? " -splicepenalty=$value" : "" 7 Cost for an intron, independent of length and starting/ending on donor-acceptor sites minscore Minimum accepted score (-minscore) 30 perl (defined $value && $value != $vdef)? " -minscore=$value" : "" 8 Exclude alignments with scores below this threshold score. reverse Reverse orientation (-reverse) perl ($value)? " -reverse" : "" 9 Reverse the orientation of the EST sequence splice Use donor and acceptor splice sites (-splice) 1 perl ($value)? "" : " -nosplice" 10 Use donor and acceptor splice sites. If you want to ignore donor-acceptor sites then set this to be false. mode Comparison mode (-mode) both perl ($value && $value ne $vdef)? " -mode=$value" : "" 11 This determines the comparion mode. The default value is 'both', in which case both strands of the est are compared assuming a forward gene direction (ie GT/AG splice sites), and the best comparsion redone assuming a reversed (CT/AC) gene splicing direction. The other allowed modes are 'forward', when just the forward strand is searched, and 'reverse', ditto for the reverse strand. best Print out only best alignment (-best) 1 perl ($value)? "" : " -nobest" 12 You can print out all comparisons instead of just the best one by setting this to be false. space Space threshold (in megabytes) (-space) 10.0 perl (defined $value && $value != $vdef)? " -space=$value" : "" 13 for linear-space recursion. If product of sequence lengths divided by 4 exceeds this then a divide-and-conquer strategy is used to control the memory requirements. In this way very long sequences can be aligned. <BR> If you have a machine with plenty of memory you can raise this parameter (but do not exceed the machine's physical RAM) shuffle Shuffle (-shuffle) perl ($value)? " -shuffle=$value" : "" 14 seed Random number seed (-seed) 20825 perl (defined $value && $value != $vdef)? " -seed=$value" : "" 15 output Output section outfile outfile (-outfile) outfile.out perl " -outfile=$value" 16 align Show the alignment (-align) perl ($value)? " -align" : "" 17 Show the alignment. The alignment includes the first and last 5 bases of each intron, together with the intron width. The direction of splicing is indicated by angle brackets (forward or reverse) or ???? (unknown). width Alignment width (-width) 50 perl (defined $value && $value != $vdef)? " -width=$value" : "" 18 auto perl " -auto -stdout" 19