[Bioperl-l] Re: Ready!
Jason Stajich
jason@chg.mc.duke.edu
Wed, 6 Jun 2001 09:25:12 -0400 (EDT)
Including the list so I won't be a single point of failure on information
or suggestions.
On Tue, 5 Jun 2001, Roger Hall wrote:
> In sub to_FTstring, when location->start == location->end, only the
> location->start value is returned by design. I would guess that this has
> more than one reason, and would not be the place to apply changes for 955.
>
Clearly not the best programming design here by me, but was trying to
handle EMBL/GenBank FeatureTable printing first as that was the thorn in
my side. Truthfully to_FTstring should only be used by embl/genbank
directly.
Couple of options, extend to_FTstring to know how to print itsself in
swiss,genbank,embl formats based on a input parameter (bad design
methodology requiring a class to know all of its users) or follow your
solution below.
I vote for adding the code in swiss::_print_swissprot_FTHelper as you
suggest. May need to do some testing with split/fuzzy locations and
swissprot feature table to make sure we handle that correctly as well
since those come from to_FTstring as well.
> my($self) = @_;
> if( $self->start == $self->end ) {
> return $self->start;
> }
> my $str = $self->start . ".." . $self->end;
> return $str;
>
> Instead, a possibly better place to handle this is in
> swiss::_print_swissprot_FTHelper. It currently assumes that there is a
> string that represents a range:
>
> $fth->loc =~ /(\d+)\.\.(\d+)/;
> $start = $1;
> $end = $2;
>
> But since to_FTstring returns only one value, and not a string that
> represents a range, no matches are found. I have solved the problem with the
> addition of this line immediately following '$end = $2;':
>
> if (!$start) { $start = $end = $fth->loc; }
>
> This assumes that if there is not a range, then there is one value, AND that
> value is the start and end of the feature range.
>
> I recommend this change if this problem is localized to Swiss, and not a
> general protein problem. Otherwise, to_FTstring might need to be rethought.
>
> Which way to go?
>
> And please verify: I should commit the change in the branch-07 branch AND in
> the bioperl-live branch...
>
yes you should since this is a bug on both branches.
> Thanks!
>
> Roger
>
> The new outut:
>
> ID 143B_BOVIN STANDARD; PRT; 245 AA.
> AC P29358;
> DT 01-DEC-1992 (Rel. 24, Created)
> DT 01-FEB-1996 (Rel. 33, Last sequence update)
> DT 30-MAY-2000 (Rel. 39, Last annotation update)
> DE 14-3-3 PROTEIN BETA/ALPHA (PROTEIN KINASE C INHIBITOR PROTEIN-1)
> (KCIP-1).
> GN YWHAB
> OS Bos taurus (Bovine), and Ovis aries (Sheep).
> OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
> Mammalia;
> OC Eutheria; Cetartiodactyla; Ruminantia; Pecora; Bovoidea; Bovidae;
> Bovinae;
> OC Bos.
> RN [1]
> RP SEQUENCE.
> RC SPECIES=Bovine;
> RX MEDLINE=91108808; PubMed=1671102;
> RA Isobe T., Ichimura T., Sunaya T., Okuyama T., Takahashi N., Kuwano R.,
> RA Takahashi Y.
> RT "Distinct forms of the protein kinase-dependent activator of tyrosine
> and
> RT tryptophan hydroxylases."
> RL J. Mol. Biol. 217:125-132(1991).
> RN [2]
> RP SEQUENCE OF 2-83; 121-186 AND 199-241.
> RC SPECIES=Sheep; TISSUE=BRAIN;
> RX MEDLINE=92283271; PubMed=1317796;
> RA Toker A., Sellers L.A., Amess B., Patel Y., Harris A., Aitken A.
> RT "Multiple isoforms of a protein kinase C inhibitor (KCIP-1/14-3-3) from
> RT sheep brain. Amino acid sequence of phosphorylated forms."
> RL Eur. J. Biochem. 206:453-461(1992).
> RN [3]
> RP SEQUENCE OF 2-23.
> RC SPECIES=Sheep; TISSUE=BRAIN;
> RX MEDLINE=90345949; PubMed=2143472;
> RA Toker A., Ellis C.A., Sellers L.A., Aitken A.
> RT "Protein kinase C inhibitor proteins. Purification from sheep brain and
> RT sequence similarity to lipocortins and 14-3-3 protein."
> RL Eur. J. Biochem. 191:421-429(1990).
> RN [4]
> RP PHOSPHORYLATION.
> RC SPECIES=Sheep;
> RX MEDLINE=95197587; PubMed=7890696;
> RA Aitken A., Howell S., Jones D., Madrazo J., Patel Y.
> RT "14-3-3 alpha and delta are the phosphorylated forms of raf-activating
> RT 14-3-3 beta and zeta. In vivo stoichiometric phosphorylation in brain
> at a
> RT Ser-Pro-Glu-Lys motif."
> RL J. Biol. Chem. 270:5706-5709(1995).
> RN [5]
> RP POST-TRANSLATIONAL MODIFICATIONS.
> RC SPECIES=Sheep;
> RA Aitken A., Patel Y., Martin H., Jones D., Robinson K., Madrazo J.,
> Howell
> RA S.
> RT "Electrospray mass spectroscopy analysis with online trapping of
> RT posttranslationally modified mammalian and avian brain 14-3-3
> isoforms."
> RL J. Protein Chem. 13:463-465(1994).
> CC -!- FUNCTION: ACTIVATES TYROSINE AND TRYPTOPHAN HYDROXYLASES IN THE
> CC PRESENCE OF CA(2+)/CALMODULIN-DEPENDENT PROTEIN KINASE II, AND
> CC STRONGLY ACTIVATES PROTEIN KINASE C. IS PROBABLY A MULTIFUNCTIONAL
> CC REGULATOR OF THE CELL SIGNALING PROCESSES MEDIATED BY BOTH
> CC KINASES.
> CC -!- SUBUNIT: HOMODIMER.
> CC -!- SUBCELLULAR LOCATION: CYTOPLASMIC.
> CC -!- ALTERNATIVE PRODUCTS: TWO FORMS ARE PRODUCED BY ALTERNATIVE
> CC INITIATION.
> CC -!- TISSUE SPECIFICITY: 14-3-3 PROTEINS ARE LOCALIZED IN NEURONS, AND
> CC ARE AXONALLY TRANSPORTED TO THE NERVE TERMINALS. THEY MAY BE ALSO
> CC PRESENT, AT LOWER LEVELS, IN VARIOUS OTHER EUKARYOTIC TISSUES.
> CC -!- PTM: ISOFORM ALPHA DIFFERS FROM ISOFORM BETA IN BEING
> CC PHOSPHORYLATED.
> CC -!- SIMILARITY: BELONGS TO THE 14-3-3 FAMILY.
> DR PIR; S13467; S13467.
> DR PIR; S10804; S10804.
> DR PIR; S23179; S23179.
> DR InterPro; IPR000308; 14-3-3.
> DR Pfam; PF00244; 14-3-3.
> DR PRINTS; PR00305; 1433ZETA.
> DR SMART; SM00101; 14_3_3.
> DR PROSITE; PS00796; 1433_1.
> DR PROSITE; PS00797; 1433_2.
> KW Brain; Neurone; Phosphorylation; Acetylation; Multigene family;
> KW Alternative initiation.
> FT INIT_MET 0 0
> FT CHAIN 1 245 14-3-3 PROTEIN BETA/ALPHA, LONG ISOFORM.
> FT CHAIN 2 245 14-3-3 PROTEIN BETA/ALPHA, SHORT ISOFORM.
> FT INIT_MET 2 2 FOR SHORT ISOFORM.
> FT MOD_RES 1 1 ACETYLATION.
> FT MOD_RES 2 2 ACETYLATION (IN SHORT ISOFORM).
> FT MOD_RES 185 185 PHOSPHORYLATION.
> SQ SEQUENCE 245 AA; 27950 MW; AA91C2314D99549F CRC64;
> TMDKSELVQK AKLAEQAERY DDMAAAMKAV TEQGHELSNE ERNLLSVAYK NVVGARRSSW
> RVISSIEQKT ERNEKKQQMG KEYREKIEAE LQDICNDVLQ LLDKYLIPNA TQPESKVFYL
> KMKGDYFRYL SEVASGDNKQ TTVSNSQQAY QEAFEISKKE MQPTHPIRLG LALNFSVFYY
> EILNSPEKAC SLAKTAFDEA IAELDTLNEE SYKDSTLIMQ LLRDNLTLWT SENQGDEGDA
> GEGEN
> //
>
>
Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center
http://www.chg.duke.edu/