]> Mutate sequence beyond all recognition (EMBOSS) nucleic:mutation protein:mutation http://bioweb.pasteur.fr/docs/EMBOSS/msbar.html msbar &emboss_init; input Input section sequence sequence -- any [sequences] (-sequence) perl " -sequence=$value -sformat=fasta" 1 any 8 seqsfile perl 1 required Required section count Number of times to perform the mutation operations (-count) 1 perl " -count=$value" 2 point Types of point mutations to perform -- Point mutation operations [select values] (-point) 0 None 1 Any of the following 2 Insertions 3 Deletions 4 Changes 5 Duplications 6 Moves , 0 perl " -point=$value" 3 block Types of block mutations to perform -- Block mutation operations [select values] (-block) 0 None 1 Any of the following 2 Insertions 3 Deletions 4 Changes 5 Duplications 6 Moves , 0 perl " -block=$value" 4 advanced Advanced section inframe Do 'codon' and 'block' operations in frame (-inframe) 0 perl ($value)? " -inframe" : "" 5 codon Types of codon mutations to perform -- Codon mutation operations [select values] (-codon) 0 None 1 Any of the following 2 Insertions 3 Deletions 4 Changes 5 Duplications 6 Moves , acd @(!$(acdprotein)) 0 perl " -codon=$value" 6 Types of codon mutations to perform. These are only done if the sequence is nucleic. minimum Minimum size for a block mutation (-minimum) 1 perl (defined $value && $value != $vdef)? " -minimum=$value" : "" 7 maximum Maximum size for a block mutation (-maximum) 10 perl (defined $value && $value != $vdef)? " -maximum=$value" : "" 8 acd $minimum othersequence Other sequences that the mutated result should not match (-othersequence) perl ($value && $value ne $vdef)? " -othersequence=$value -sformat=fasta" : "" 9 If you require that the resulting mutated sequence should not match a set of other sequences, then you can specify that set of sequences here. For example, if you require that the mutated sequence should not be the same as the input sequence, enter the input sequence here. If you want the result to be different to previous results of this program, specify the previous result sequences here. The program will check that the result does not match the sequences specified here before writing it out. If a match is found, then the mutation is started again with a fresh copy of the input sequence. If, after 10 such retries, there is still a match to the set of sequence given here, then the matching mutated sequence is written with a warning message. any 8 output Output section outseq outseq (-outseq) outseq.out perl " -outseq=$value" 10 seqsfile perl 1 outseq_sformat Output format for: outseq fasta fasta gcg gcg phylip phylip embl embl swiss swiss ncbi ncbi nbrf nbrf genbank genbank ig ig codata codata strider strider acedb acedb staden staden text text fitch fitch msf msf clustal clustal phylip phylip phylip3 phylip3 asn1 asn1 fasta perl " -osformat=$value" 11 auto perl " -auto -stdout" 12