On Tuesday 14 June 2005 16:37, Wagner, David --- Senior Programmer Analyst ---
WGO wrote:
[...]
> > I have this (pertinent) code in my script:
> >
> > $dnakmotif ='[KRH][L{3,}V{3,}I{3,}F{3,}Y{3,}A{3,}][KRH];
>
> $dnakmotif ='[KPH](L{3,5}|V{3,5}|I{3,5}|F{3,5}|Y{3,5}|A{3,5}){1,}[KRH]';
> This should allow some thing to start with KPH and have one or more of the
> series of LVIFYA at least 3 and no more than 5 and ending with KRH.
>
> Wags ;) ps not tested. A sample of data would hve been nice.
[...]
Oh yes, here is a sequence I am using:
>gi|9911089|sp|P03764|STF_LAMBD Side tail fiber protein
MAVKISGVLKDGTGKPVQNCTIQLKARRNSTTVVVNTVGSENPDEAGRYSMDVEYGQYSVILQVDGFPPS
HAGTITVYEDSQPGTLNDFLCAMTEDDARPEVLRRLELMVEEVARNASVVAQSTADAKKSAGDASASAAQ
VAALVTDATDSARAASTSAGQAASSAQEASSGAEAASAKATEAEKSAAAAESSKNAAATSAGAAKTSETN
AAASQQSAATSASTAATKASEAATSARDAVASKEAAKSSETNASSSAGRAASSATAAENSARAAKTSETN
ARSSETAAERSASAAADAKTAAAGSASTASTKATEAAGSAVSASQSKSAAEAAAIRAKNSAKRAEDIASA
VALEDADTTRKGIVQLSSATNSTSETLAATPKAVKVVMDETNRKAPLDSPALTGTPTAPTALRGTNNTQI
ANTAFVLAAIADVIDASPDALNTLNELAAALGNDPDFATTMTNALAGKQPKNATLTALAGLSTAKNKLPY
FAENDAASLTELTQVGRDILAKNSVADVLEYLGAGENSAFPAGAPIPWPSDIVPSGYVLMQGQAFDKSAY
PKLAVAYPSGVLPDMRGWTIKGKPASGRAVLSQEQDGIKSHTHSASASGTDLGTKTTSSFDYGTKTTGSF
DYGTKSTNNTGAHAHSLSGSTGAAGAHAHTSGLRMNSSGWSQYGTATITGSLSTVKGTSTQGIAYLSKTD
SQGSHSHSLSGTAVSAGAHAHTVGIGAHQHPVVIGAHAHSFSIGSHGHTITVNAAGNAENTVKNIAFNYI
VRLA
Originally I had thought to assign L, I, V, F, Y, and A to another variable,
called $hydrophobe or some such and simply see about looking for a series of
hydrophobes between K, R, or Hs between 3 to 5 characters in length but could
not figure out a way to do this in Perl. I am using a Perl book called
"Beginning Perl for Bioinformatics" and it doesn't appear to have anything in
it along the line of what my original desire was.
praedor
--
"Voice or no voice, the people can always be brought to the bidding of
the leaders. That is easy. All you have to do is tell them they are
being attacked, and denounce the peacemakers for lack of patriotism and
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--Hermann Goering
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