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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: [log in to unmask] ============================ 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 <[log in to unmask]>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: [log in to unmask] > ******************************************* >