Good *free* primer/restriction progam

[mark-ER]

Yo,

Just need a bit of feedback: I've been using some really old software (1998 version of Vector-NTI) to search for PCR & qRT-PCR primers, as well as analyzing sequence for enzyme restriction sites. I think it's time to get with the times and update. What are you guys using?

I'd prefer something that's free/open access, perhaps available online, but would consider something that I'd have to pay for, if it's relatively commonly used has lots of desirable features & relatively cheap.

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[phenylrabbid]

For general sequence analysis (from viewing ABI files to RE digest maps) I use BioEdit ( http://www.mbio.ncsu.edu/BioEdit/bioedit.html ). It's free (as in beer, not speech), and can run using WINE if you are using linux (It's a MS-Windows based app).

Another good site for finding useful programs/projects is bioinformatics.org .

Hope this helps.

 

[j-weezy]

Yo,

Just need a bit of feedback: I've been using some really old software (1998 version of Vector-NTI) to search for PCR & qRT-PCR primers, as well as analyzing sequence for enzyme restriction sites. I think it's time to get with the times and update. What are you guys using?

I'd prefer something that's free/open access, perhaps available online, but would consider something that I'd have to pay for, if it's relatively commonly used has lots of desirable features & relatively cheap.

ApE plasmid editor....it's awesome!!! It's also free! just type ApE plasmid into google and it'll come up with a link

 

[byong_soo]

ApE

 

[IgnisDU]

I asked this same question (except for macs) on livejournal the other day.

here is the link

http://community.livejournal.com/_scientists_/867022.html

 

[j-weezy]

I asked this same question (except for macs) on livejournal the other day.

here is the link

http://community.livejournal.com/_scientists_/867022.html

ApE works on macs also - it's platform independent (i think i'm using this term correctly...)

I almost feel like a walking, talking advertisement for ApE but it's just because it's made my life so much easier!

 

[MrMunkily]

ApE's web page says that development is probably going to be discontinued... due to "legal" issues. Anyone know why?

 

[j-weezy]

ApE's web page says that development is probably going to be discontinued... due to "legal" issues. Anyone know why?

Only guessing here....perhaps treading on the toes of biotech companies? I've only seen a couple of other programs but I think at a certain level all of these primer/restriction/sequence alignment programs have certain design/programming aspects in common. Because of this I can easily see some biotech company (ie. Invitrogen - although I think they only charge commercial researchers) getting angry that a product/service they're charging people for is easily and freely acquired elsewhere. There was a link on the website to the individual's blog - it looks like he/she used to work for a software development company so there may be issues there as well. I'm downloading the most up to date version and keeping my fingers crossed that these issues resolve themselves - but definitely not holding my breath.

 

[psymedicus]

This page has several PCR/RFLP related tools, it's really good.

http://bioinfo.bsd.uchicago.edu/index.html

 

[mjs]

ApE is good for plasmids.

WebCutter or NEBCutter are good for restriction analysis.

Primer3 is good for primer selection. It claims to work for probe selection, but I can't speak for it.

Pa Google will tell you where to find them.

 

[NGN47]

For qRT-PCR primers, I also suggest using primer3. It has almost always worked well for me. Try to select primer pairs that span exon junctions, though, to reduce the chances for genomic sequence amplification. Good luck!