Thanks everybody, I tried using --toolkit tuebingen mpi --Scanprosite
I think my regex syntax was different from the Tuebingen site's, but scanprosite worked well and found many hits, although without really hitting paydirt. I think both of these programs would do the job well, though. Thanks very much for your speedy help (this BB is truly amazing!), Jacob On Tue, Oct 4, 2011 at 3:47 PM, David Briggs <[email protected]> wrote: > Hi Jacob, > SCAN PROSITE > http://prosite.expasy.org/scanprosite/ > will do precisely what you want. > C-X-C-X-C-X-C > or > C-X-C-X-C > would be the pattern using Prosite syntax. > Cheers, > Dave > ============================ > David C. Briggs PhD > Father, Structural Biologist and Sceptic > ============================ > University of Manchester E-mail: > [email protected] > ============================ > http://manchester.academia.edu/DavidBriggs (v.sensible) > http://xtaldave.wordpress.com/ (sensible) > http://xtaldave.posterous.com/ (less sensible) > Twitter: @xtaldave > Skype: DocDCB > ============================ > > > On 4 October 2011 21:34, Jacob Keller <[email protected]> > wrote: >> >> Dear Crystallographers, >> >> I cannot get BLAST to find all proteins with the motif cxcxcxc or at >> least cxcxc. It seems to think of "x" as an actual amino acid rather >> than a wildcard. There must be some easy way to do this? Ordinarily to >> find a short motif, I would just paste the sequence and get the >> answer, but here the C's are an absolute requirement and there is no >> constraint on the x's except that they be only one residue. >> >> JPK >> >> -- >> ******************************************* >> Jacob Pearson Keller >> Northwestern University >> Medical Scientist Training Program >> cel: 773.608.9185 >> email: [email protected] >> ******************************************* > > -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: [email protected] *******************************************
