> Maybe it's just a sequencing glitch? Not so--BLAST showed there are a whole cadre of these things in various genomes. Go figure.
JPK > > JPK > > > On Tue, Oct 4, 2011 at 4:05 PM, Jacob Keller > <[email protected]> wrote: >> 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] >> ******************************************* >> > > > > -- > ******************************************* > 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] *******************************************
