Thanks Suku - forgot about the P1, F1 stuff. Still don't understand why you just can't use the simpler FASTA format with all these programs, or even just a plain text file!
Tony. Sent from my iPhone On 12 Aug 2011, at 10:18, "sukanta mondal" <sukanta.mon...@gmail.com<mailto:sukanta.mon...@gmail.com>> wrote: NBRF/PIR Format: A sequence in PIR format consists of: 1. One line starting with * a ">" (greater-than) sign, followed by * a two-letter code describing the sequence type (P1, F1, DL, DC, RL, RC, or XX), followed by * a semicolon, followed by * 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 <<mailto:p...@mrc-lmb.cam.ac.uk>p...@mrc-lmb.cam.ac.uk<mailto:p...@mrc-lmb.cam.ac.uk>> 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" > <<mailto:p...@mrc-lmb.cam.ac.uk>p...@mrc-lmb.cam.ac.uk<mailto:p...@mrc-lmb.cam.ac.uk>> > 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/> >>> http://smb.slac.stanford.edu/jcsg/QC/ >>> >>> >>> >>> >>> >>> >>> On Thu, Aug 11, 2011 at 4:58 PM, Jacob Keller >>> <<mailto:j-kell...@fsm.northwestern.edu>j-kell...@fsm.northwestern.edu<mailto:j-kell...@fsm.northwestern.edu>> >>> wrote: >>> I think they fudged the data in this paper... >>> >>> JPK >>> >>> On Thu, Aug 11, 2011 at 6:30 PM, David Schuller >>> <<mailto:dj...@cornell.edu>dj...@cornell.edu<mailto:dj...@cornell.edu>> >>> wrote: >>>> link: <http://iai.asm.org/cgi/reprint/IAI.05661-11v1> >>>> 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 >>>> <mailto:schul...@cornell.edu> >>>> schul...@cornell.edu<mailto:schul...@cornell.edu> >>>> >>> >>> >>> >>> -- >>> ******************************************* >>> Jacob Pearson Keller >>> Northwestern University >>> Medical Scientist Training Program >>> cel: 773.608.9185<tel:773.608.9185> >>> email: <mailto:j-kell...@northwestern.edu> >>> j-kell...@northwestern.edu<mailto:j-kell...@northwestern.edu> >>> ******************************************* >>>
