Multimprimer3 is automated web-based primer design tool for primer design from bacterial repetitive DNA sequences
Multimprimer3 designs detection PCR primers for bacteria. There is two options how to use Multimprimer3.
- User knows the names of bacterial species/genomes which he/she wants to detect (with one primer pair and in one sample). These names can be selected
from given list (the strains, species and genera in our local database are given here). Also, user can choose non-target bacterial species/genomes that may occur in
the sample. Additionally, human genomic sequence can be chosen as non-target genome (by
inserting checkmark to checkbox 'Homo sapiens as non-target genome'). Currently, the genomic
sequences are retrieved from NCBI (only completed genomes are retrieved).
The email address may be inserted in case of time consuming tasks (if many bacterial genomes
and/or human genomic sequence is chosen). Finally,
general primer design options (flags of primer3) can be specified.
Thereafter, the program looks for
3 target-specific repetitive DNA sequences that
- are present each at least as two different copies in each target genome (if no repetitive sequence is found then target-specific sequence with one copy is considered)
- not present in non of the non-target genomes
After that queried number ofPrimers are not assessed with any score; primer pairs are ought to be equally well working. User gets DNA sequences of PCR primers and
PCR products, genomic positions of repetitive sequences which are used for primer design and some additional
data about users query and primer design.
- PCR primers are designed to consensus sequence of each repetitive sequences with primer3
- Target-specificity of designed primers is checked with fastagrep (primers must not amplify sequences from non-target genomes)
- User has his/her own (repetitive) sequence. The sequence must be in FASTA format. If there is more than one sequence primers
will be designed to the consensus sequence composed from inserted sequences. Principally, the process
for finding PCR primers for the repeat is the same as described above. The uniqueness of inserted sequence(s) is (are)
checked against selected non-target genomes and the uniqueness of designed primers is examined.