I am looking for a software program that can analyze a protein coding region of DNA and find where restriction sites can be added without changing the coding sequence. I did find the program SiteFind, but the website for it does not appear to be working.
Danilo, I am familiar with NEBcutter but did not see an option for that in it, will look into DNAMAN.
SiteFind is exactly what you want, but it has a problem with many web browsers. It's set up as a Java application, but most browsers won't open it because of the security settings. This is due to a change in the security policies in recent versions of Java.
To run SiteFind, you need to tell Java on your computer that it's okay to run "unsigned" applications on that specific site. Two places that describe how to do this are here:
https://www.java.com/en/download/help/java_blocked.xml
http://derflounder.wordpress.com/2014/01/15/oracle-java-7-update-51-blocks-unsigned-java-applets-by-default/
It's a simple application, but it works well.
Here another online option: http://www.insilicase.co.uk/Web/Mutagenesis.aspx
Hi Thomas,
I tried doing everything I could to get Sitefind to run, and it still would not. The Java settings I see are different than the tutorials on how to fix the issue, Java wants me to import a certificate.
Hi Thomas,
Okay, Java must of updated itself and I was able to get SiteFind to run after adding it to the site list. SiteFind can take longer seq. (do not know how long, but at least 72 bp) than Insilicase which has a 66 bp limit, but for SiteFind you have to enter the sequence by hand (could not copy/paste), while with Insilicase you can copy/paste in seq. Also I could not copy/paste the results from SiteFind into a Word doc. while I could do that with Insilicase. But hey they are both free!
Thanks
I compared SiteFind and Insilicase on the same 24 bp DNA sequence:
SiteFind found 12 RE that could be engineered in "without" a change to the AA sequence. SiteFind only lists RE sites that do "not" change the AA sequence.
Insilcase found only one RE that did not change the AA sequence, but listed lots of RE that changed the AA sequence.
And what was interesting is Insilcase did not list the RE that SiteFind found. So for me SiteFind is the way to go.
The issues with SiteFind are all due to recent changes in Java and the way it handles applications. Java was changed to increase security (and prevent web-sites from doing damage to your computer). Unfortunately, it makes the application much harder to set up and use. It may be possible to tweak the settings on your local computer to make cut and paste possible. I have had it working in the past, but not consistently.
The real solution is for someone who knows a bit of Java (and has the proper tools) to make it comply with the new security arrangements that Java has implemented. The source code is available here: http://www.bioinformatics.org/project/?group_id=533 I'd love to, but my programming skills are quite out of date.
Hi Marta,
I have been using SerialCloner and found the silent map tab, Thanks!
So I should say that of the three programs: SiteFind, Insilicase, and SerialCloner, SerialCloner is the best for finding silent RE sites (I analyzed a 6,000 bp sequence with it), plus it can run PCR reactions to make sure your primers are good!, and it can do a lot more.
I like that program a lot too. So far it has been the best one I have used and honestly they are not paying me for advertising.
Sorry, but I cannot follow, how can it be done with Serial Cloner ? Is there a such feature in the menu? - I couldn't find it.
Thanks in advance for the comments on that !
The easiest but perhaps not the most effective way is tehe NEBcutter ("Silent Mutagenesis" section) for example :
http://nc2.neb.com/NEBcutter2/silmut.php?name=0a350124-&orfid=1
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