Software for scanning of specific aa sequence in proteins - (Jan/11/2013 )
I was wondering if there is a software or a database (free preferably) that is able to scan for the presence of specific amino acid sequences/ motifs in proteins. I am interested in finding a phosphodegron motif. It would be cool if the accessibility to this motif could be measured (put it in the context of secondary and tertiary structure), but this feature is not crucial, since I can potentially check it later (it will be more labor-intensive though). Thanks in advance for any comments.
you can BLAST it against sequence of interest
Thank you for your suggestions. I was kind of hoping that there is something more high throughput, but I guess I'll just make a list of possibilities and go one-by-one. I'll also perform a more thorough search for available software (free or paid) over the next month and will post if I find something and describe my experience using it. Thanks once again.
As I said I tried using blast, but it seems pretty useless for screens. I found this software, which has its limitations as well, but is quite useful and is an excellent starting point:
It is really easy to use and you can just copy the results into excel and create tables you can browse at your convenience. Most importantly, it is free.
You should also check out the Nucleic Acids Research online database and web server issues (both online on their webpage), which may contain a few potential sites that you missed.