Create Intron Spanning primers
What you can do:
Automated pipeline for RT-PCR primer design, targeted to span intronic sequences.
Highlights:
- Supported organism are human, mouse, rat and fruitfly.
- This tool specifically tries to design Realtime-primers spanning introns.
- Primers are not targetted to exon-exon boundaries.
- The resulting amplicons should only amplify cDNA sequences if the intron size is large enough and/or extension time is limited.
- The sequences are fetched from UCSC databases, based on regions corresponding to the supplied RefSeq Symbol.
- Next, primers will be tested on each of introns to check if they form primer dimers and hairpin structures, have an acceptable GC-content and melting temperature.
- Acceptable primers are then combined to form amplicons. Amplicons of acceptable size are then folded used mfold to check for secondary structures and blasted against the refseq_RNA database to check specificity.
- A short summary is provided listing the primers, the amplicon and all targets (multiple targets are allowed if they are isoforms of the same gene).
Keywords:
- PCR primers
- oligos databases
- design tools
- intron
- RT-PCR
This record last updated: 12-13-2012