C. elegans primer design

C. elegans primer design

A specific primer design program for C. elegans genes modified from MPprimer.

C. elegans primer design: a specific primer design program for C. elegans genes modified from MPprimer. It employs the widely used primer design program Primer3 [Rozen, et al. 2000] and primer specificity evaluation program MFEprimer [Qu, et al. 2009] to design and evaluate the candidate primers based on genomic or transcript DNA database.

Input the sequence in FASTA format or just input a gene name (fipr-24), a GenePairs name (C37A5.8) or a WB gene ID (WBGene00007992).

Example input sequences

Paste source sequence(s) as DNA templates for primer sets design for PCR in FASTA format below (5'->3', string of ACGTNacgtn -- other letters treated as N -- numbers and blanks ignored).
MPprimer also support for conventional PCR primer design by pasting one sequence.

Or upload the sequence file in FASTA format from disk:

Primer specificity check settings (Optional).

The database is used to check the specificity of the PCR primer as described in MFEprimer paper(Qu et al., 2009, Bioinformatics, 25(2), 276-278). To be noticed that, for the Multiplex PCR reaction, the database here is not only used to check the specificity of the pair of primers (forward and reverse primer), but also to check the cross-reaction among primers, for example, to check the primer A (from template A) and primer B (from template B) whether has the ability to initial a PCR reaction. Although this is optional, it's strongly suggested that users should choose a database before picking the primers.

Select database:	Word size for BLASTN	E-value for BLASTN

E-value is a parameter used in NCBI BLAST (Altschul SF et al. J Mol Biol. 1990 Oct 5;215(3):403-10). MFEprimer uses NCBI BLAST to check the sequence similarity between primers and the DNA templates. By using a larger E-value, BLAST would report more hits. As a result, MFEprimer would be more sensitive. CAUTION: MPprimer would collapse if the E-value is too large. The default value is recommended.

Word size is a parameter used in NCBI BLAST (Altschul SF et al. J Mol Biol. 1990 Oct 5;215(3):403-10). MFEprimer uses BLAST to check the sequence similarity between primers and the DNA templates. With smaller word size, BLAST would report more hits. As a result, MFEprimer would be more sensitive. CAUTION: MPprimer would collapse if the Word size is too small. The default value is recommended.

Primer pick settings (Optional).

These are the general primer picking conditions for each DNA sequence to generate candidate primers.

Primer Tm:	Min:	Opt:	Max:	Max 3' stability
Primer Size:	Min:	Opt:	Max:	Max self complementarity:
Primer GC%:	Min:	Opt:	Max:	Max 3' self complementarity:
Concentration of monovalent cations (usually KCl, mM)				Concentration of divalent cations (usually MgCl₂, mM)
Concentration of dNTPs (mM)				Annealing oligo concentration (nM)
Target region:
Product Size Ranges: