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 <[log in to unmask]> 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:
> [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]
>> *******************************************
>
>
--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
cel: 773.608.9185
email: [log in to unmask]
*******************************************
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