HOW-TO:
- The sequences should be formatted in FASTA format, all the sequences should be stored one after the other
in 1 big pure ASCII text file
(word documents are binary files, not pure ASCII text!! and won't work, neither are excel sheets etc)
eg.
>sequence_1
ACGTAGCGATAAGCAGGACTACAACGCACGAATATCAGCAGCACTCTACAGCAGTA
ACGATAGACGATACAGATACACTACTACTATAGACGATTCTCTCGACGAGACTACA
AAACT
>sequence_2
ACGATAGACGATACAGATACACTACTACTATAGACGATTCTCTCGACGAGACTACA
ACGTAGCGATAAGCAGGACTACAACGCACGAACTATAGACGATTCTCTTGACTA
- The motif recognized by the restriction enzyme should be given (see also IUPAC code below). Not the name of the enzyme!
= the position of the cut can be given with a '^' (eg R^GATCY), but is only used with the DIGEST option
= for TPF (cDNA-AFLP) and AFLP no exact cut is used, but each fragment returned begins and ends with the whole site
as recognized by one of the used enzymes.
= for the DIGEST exact place of the cut is added, but still the whole site is included
- The extended genetic code can be used for the restriction sites... The order of the sites is important, especially for cDNA-AFLP
- For the selective nucleotides N will act as 'no selective nucleotide'
There is no real limit on the size of sequences one can submit (the whole genome (120Mb) of Arabidopsis works fine)
IUPAC = "A" => "A"
"C" => "C"
"G" => "G"
"T" => "T"
"U" => "T"
"M" => "(A/C)"
"R" => "(A/G)"
"W" => "(A/T)"
"S" => "(C/G)"
"Y" => "(C/T)"
"K" => "(G/T)"
"V" => "(A/C/G)"
"H" => "(A/C/T)"
"D" => "(A/G/T)"
"B" => "(C/G/T)"
"N" => "(A/C/G/T)"
"X" => "(A/C/G/T)"
BUG REPORT: report to
me
26/02/2002 Frank (frbre) reported problem with selective nucleotides (solved)
22/08/2003 bug reported (in new version) about some fragments that still had a restriction site within the fragment (solved)
alternatively you can also visit In-silico.com
for bacterial genomes only.