Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-10-26

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All times shown according to UTC.

Time Nick Message
00:21 art joined #bioperl
00:22 art hey guys
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14:39 DanC joined #bioperl
14:40 DanC I'm writing code to grab Pfam/SCOP/CATH residue coordinates from SIFTS data, but struggling with coordinate systems. Anybody here familiar with SIFTS?
14:40 DanC SIFTS as in http://www.ebi.ac.uk/pdbe/docs/sifts/ or http://www.ncbi.nlm.nih.go​v/pmc/articles/PMC540012/
14:51 ende joined #bioperl
14:54 * ende :waves
15:12 DanC ende, any chance you've worked with SIFTS XML? (http://www.ebi.ac.uk/pdbe/docs/sifts/ )
15:13 DanC anybody have suggestions for other sources of PFam/SCOP/CATH data in bulk?
15:14 ende I haven't
15:14 ende but im reading it right now
15:14 ende So it's basically a way of relating similar entities across different databases?
15:15 DanC yes
15:15 ende That could be useful
15:15 DanC All I really need is start/end coordinates for features of PDB structures, given a PDBID
15:16 DanC SIFTS seems to provide it, but I can't understand how their coordinates work.
15:17 DanC in particular, the segment element: http://www.efamily.org.uk/xml/efam​ily/documentation/efamily.shtml#3
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