Recent changes to feature-requests

intron sizes

Anonymous — Sat, 07 Apr 2012 07:02:10 -0000

I find this program is a leading one when it comes to primer design for RT-PCR because of its nice feature to include options for intron spanning regions. My request would be of course is to improve this property and include the sizes of each intron, total bps of introns in a primer set can be listed along with other characteristics of the primer set like the amplicon length and Tm, etc. and thank you in advance.

Position selection

lewis collins — Fri, 11 Mar 2011 13:29:40 -0000

I really like the program, it's very useful and gives lots of options when designing primers. However, there is one thing I thought would be useful, certainly for me of late. Sometimes, it is necessary to design primers to specific regions and positions. I'm currently using primers to confirm RNAi knockdown in Drosophila and to assess inadvertent knockdown of other genes. I was wondering if it would be possible to create an option that would allow to select more specifically, e.g. to design the 5' primer between position 100-150 and the 3' primer somewhere between 250-300.

When designing these primers, it is important that the forward and reverse flank the area of interest and try to maintain a reasonable product length, certainly <1000bp

Define included/excluded regions

Anonymous — Tue, 28 Jul 2009 15:17:37 -0000

Hello,
would it be possible to force design of primers on different exons (within qPCR design)?
Additionally, it would be cool to define regions to be included/excluded from designing primers annealing to.
Thanks

trouble retrieving the sequence from Ensembl

Anonymous — Fri, 12 Jun 2009 22:57:05 -0000

I am getting an error message when I try to find the gene_id from the Ensemble server. The error message "Unable to find gene_id in response from server. This probably means that the Ensembl server has changed formats-please report this..."

Primers from intergenic regions

Anonymous — Thu, 14 May 2009 21:17:52 -0000

Hi,
I use Perlprimer quite a lot and I like it very much, especially for making qPCR primers. Since we are also investigating promoters, it would be really cool, to have the option to retrieve sequences from the 5' and the 3' end of genes alone or together with the genomic sequence. Its of course possible to copy +paste this data into Perlprimer but it would be much more convinient if a direct download would be possible.

Hairpin calculator

Anonymous — Wed, 12 Nov 2008 20:08:19 -0000

Hello,

Will there be primer hairpin checking implemented in future releases? mFold or something like that?

Thanks

Intron size for RT-PCR

Anonymous — Wed, 08 Oct 2008 14:29:52 -0000

Hi,
Thanks for a good program! I find it the best solution for designing Q-PCR primers. However it is a bit annoying that you have to check every primer pair manually to confirm that the intron they span is big enough. If you ever make any improvements in the program, one showing the intron sizes or an option to set minimum intron size would be greatly appreciated!

Best, Maria Frank
Karolinska institutet

Proxy authentication support

Anonymous — Tue, 27 Nov 2007 03:46:40 -0000

Could you please add support for a proxy server that requires authentication.
I get the following error with ver 1.14 when I try to access Ensembl:

"Error: 407 Proxy Authentication Required (The ISA Server requires authorization to fulfill the request. Access to the Web Proxy service is denied.)"

Thanks

Alberto Catalano
acatalan@mail.usyd.edu.au

Sequencing Amorce

MGS_SUR — Wed, 27 Jun 2007 09:37:21 -0000

Hello,

I want to design primers for sequencing with PerlPrimer. Unfortunately, I only find forward primer and no reverse primer.

Is it normal or is there an option to find them?

Thanks in advance.

Regards,

Sequencing Amorce

Anonymous — Wed, 27 Jun 2007 09:29:27 -0000

Hello,

I want to design primers for sequencing with PerlPrimer. Unfortunately, I only find forward primer and no reverse primer.

Is it normal or is there an option to find them?

Thanks in advance.

Regards,