NBRF/PIR Format:
A sequence in PIR format consists of:
1. One line starting with
1. a "*>*" (greater-than) sign, followed by
2. a two-letter code describing the sequence type (P1, F1, DL, DC, RL,
RC, or XX), followed by
3. a semicolon, followed by
4. the sequence identification code (the database ID-code).
2. One line containing a textual description of the sequence.
3. One or more lines containing the sequence itself. The end of the
sequence is marked by a "***" (asterisk) character
Sequence type -> Code
--------------------------------
Protein (complete) -> P1
Protein (fragment) -> F1
DNA (linear) -> DL
DNA (circular) -> DC
RNA (linear) -> RL
RNA (circular) -> RC
tRNA -> N3
other functional RNA -> N1
Example:
>P1;CRAB_ANAPL
ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR
SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH
GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ
SDVPERSIPI TREEKPAIAG AQRK*
hope this info helps
suku
On Fri, Aug 12, 2011 at 6:11 PM, Phil Evans <[email protected]> wrote:
> That's what I had
>
> > protein
>
> GSP etc
> ...
> SEN*
>
>
> On 12 Aug 2011, at 09:19, Antony Oliver wrote:
>
> > PIR is fairly similar to Fasta, from addled memory the format is...
> >
> >> protein name;
> > ----empty line----
> > MPREIL...rest of amino acid sequence with an optional asterisk to mark
> the sequence end.
> >
> > Tony
> >
> > Sent from my iPhone
> >
> > On 12 Aug 2011, at 09:14, "Phil Evans" <[email protected]> wrote:
> >
> >> Can anyone get this server to work? For me it keeps complaining that my
> sequence file is not a PIR file. The file looks OK to me, but I've never
> really understood what a PIR file is
> >>
> >> Phil
> >>
> >> On 12 Aug 2011, at 01:39, Kevin Jin wrote:
> >>
> >>>
> >>> Should we really have some crystallographers to review and qc those
> structures before the formal releasing? JCSG has set a very good mechanism
> for this issue.
> >>>
> >>> There is a sever for self check.
> >>>
> >>> http://smb.slac.stanford.edu/jcsg/QC/
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Thu, Aug 11, 2011 at 4:58 PM, Jacob Keller <
> [email protected]> wrote:
> >>> I think they fudged the data in this paper...
> >>>
> >>> JPK
> >>>
> >>> On Thu, Aug 11, 2011 at 6:30 PM, David Schuller <[email protected]>
> wrote:
> >>>> link: http://iai.asm.org/cgi/reprint/IAI.05661-11v1
> >>>>
> >>>> Ferric C. Fang & Arturo Casadevall
> >>>> Retracted Science and the Retraction Index
> >>>> Infec. Immun. doi:10.1128/IAI.05661-11
> >>>>
> >>>> Abstract: Articles may be retracted when their findings are no longer
> >>>> considered trustworthy due to scientific misconduct or error, they
> >>>> plagiarize previously published work, or are found to violate ethical
> >>>> guidelines. Using a novel measure that we call the “retraction index,”
> we
> >>>> found that the frequency of retraction varies among journals and shows
> a
> >>>> strong correlation with the journal impact factor.
> >>>> ...
> >>>>
> >>>> (with special attention to Figure 1, Retraction Index vs. Impact
> Factor)
> >>>>
> >>>>
> >>>> --
> >>>>
> =======================================================================
> >>>> All Things Serve the Beam
> >>>>
> =======================================================================
> >>>> David J. Schuller
> >>>> modern man in a post-modern world
> >>>> MacCHESS, Cornell University
> >>>> [email protected]
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> *******************************************
> >>> Jacob Pearson Keller
> >>> Northwestern University
> >>> Medical Scientist Training Program
> >>> cel: 773.608.9185
> >>> email: [email protected]
> >>> *******************************************
> >>>
>
