After designing my own primers, how can I confirm and generate their desired location on sequence is perfect (Primer map)? Can someone suggest any other free and easy software available online?
Query sequence 33 - caacaggtaagagccgtgtgagttgtatccaccgggtagactcccacgcgggcgaggagggtcggccggtcttcgaagctacgaa - 117
REV Primer: atccaccgggtagactcccacgc
FW: acaactcacacggctcttacctgttg
you can use UCSC PCR
http://genome.ucsc.edu/cgi-bin/hgPcr?command=start
select the papameters appropriately
add FW & REV primers
and submit
in the result page you will find the fasta sequence along with the length of the product
if you click the link you can actually visualize the location of the sequence on on the chromosome
for example
FD primer: TAACAGATTGATGATGCATGAAATGGG
REV primer: CCCATGAGTGGCTCCTAAAGCAGCTGC
in human
you will find the pages like below:
Hi!
You can use NCBI Primer BLAST server to test your primers.
You can even design your primers using that server.
Go to this link:
http://www.ncbi.nlm.nih.gov/tools/primer-blast/
The form is self explanatory.
Best of luck.!!
you can use UCSC PCR
http://genome.ucsc.edu/cgi-bin/hgPcr?command=start
select the papameters appropriately
add FW & REV primers
and submit
in the result page you will find the fasta sequence along with the length of the product
if you click the link you can actually visualize the location of the sequence on on the chromosome
for example
FD primer: TAACAGATTGATGATGCATGAAATGGG
REV primer: CCCATGAGTGGCTCCTAAAGCAGCTGC
in human
you will find the pages like below:
I would like to add that I didn't find a way to provide own sequence to UCSC PCR.
That is a limitation.
Please tell me if I missed something.
@ Aditya :
UCSC PCR. can only check the primer you have, can actually fetch your desired sequence or not . It would not generate any primer for your sequence. for that you know the best tool...."NCBI Primer BLAST"
Hi;
unfortunately I can not get my genome sequence from that link. it's limited to few spp.
Could you please let me know is there any other website / software to get PCR primer map after provide, my own interest genome, FW & REV primer.
I got to know good s/w "SeqBuilder" unfortunately it's not free :(
http://www.dnastar.com/t-tutorials-seqbuilder.aspx
if anyone know similar fuction free s/w or website let me know big help !!!
I wanna obtain this type of map where primers locate in genome.
Http://www.geneinfinity.org/sms/sms_primermap.html
http://www.bioinformatics.org/sms2/primer_map.html
http://web086.unito.it/chimifm/tools/sms2/primer_map.html
In my opinion I prefer NCBI primer blast, because there are many functions and options. You can optimize your primers sequence and verify into the alignment. Best regards
http://www.bioinformatics.org/sms2/primer_map.html
I find this site very useful it is the closest you will get to manipulating the sequences
manually
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