Primer Specificity
4
1
Entering edit mode
13.7 years ago
Surendra ▴ 10

how can i determine primer (upto 10bp) specificity in genome(prokaryotic and eukaryotic)?

primer • 11k views
ADD COMMENT
0
Entering edit mode
ADD REPLY
3
Entering edit mode
13.7 years ago

For genomes available via the UCSC genome browser, you can use the In Silico PCR tool.

ADD COMMENT
2
Entering edit mode
13.7 years ago

Did you try Primer-Blast?

Primer-BLAST was developed at NCBI to help users make primers that are specific to the input PCR template. It uses Primer3 to design PCR primers and then submits them to BLAST search against user-selected database. The blast results are then automatically analyzed to avoid primer pairs (all combinations including forward-reverse primer pair, forward-forward as well as reverse-reverse pairs) that can cause amplification of targets other than the input template.

ADD COMMENT
0
Entering edit mode
ADD COMMENT
0
Entering edit mode

Please use the new server: http://www.mfeprimer.com/

ADD REPLY
0
Entering edit mode
7.7 years ago
Felix Francis ▴ 600

Try ThermoAlign: A primer design tool for tiled amplicon sequencing (includes multiplexing) using highly specific primers.

Manuscript: http://www.nature.com/articles/srep44437

https://github.com/drmaize/ThermoAlign

ADD COMMENT

Login before adding your answer.

Traffic: 2888 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6