From: Karen E. <kei...@ge...> - 2011-09-30 21:07:34
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This would not work for the beginning and end exon if they contain UTR. You can search for cds on miso and it works http://www.sequenceontology.org/browser/obob.cgi The default for the wiki does not allow searches on 3 letters or less. --Karen On 9/30/11 3:03 PM, "Keith Bradnam" <krb...@uc...> wrote: Thinking about it some more, I see that the term 'coding exon' (SO:0000195) also seems applicable: def: "An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke] Although a coding exon is listed as part of an 'exon' but not 'CDS'. Are there scenarios where a 'coding exon' wouldn't be the same thing as a CDS (segment)? Regards, Keith P.S. I noticed that if you search for 'cds' on the SO website, it returns no results On Fri, Sep 30, 2011 at 1:51 PM, Karen Eilbeck <kei...@ge...> wrote: Keith, If we wanted to fix this without making people cry, we could add a term full_cds to be the whole thing. This would leave the split line cds the same. But that will probably make a different set of people cry. --K On 9/30/11 2:48 PM, "Keith Bradnam" <krb...@uc... <http://krb...@uc...> > wrote: Hi, I think you're right Karen, but Kevin's raised a good point. In a bacterial genome annotation (or in a single-exon eukaryotic gene), you could use one GFF line to represent an entire CDS sequence. This would be consistent with the SO definition. It strikes me that most GFF3 files are using 'CDS' to really represent what is more strictly a 'CDS segment' (a sequence that has a parent 'CDS'). I'm not sure whether the duality in how 'CDS' is currently used means that it is not going to be something that is easily changed (not without breaking lots of existing code and making grown bioinformaticians cry). Regards, Keith P.S. Personally, I would like to see the addition of something like 'CDS_segment' as a new SO term to remove any confusion (apart from the confusion created by changing the status quo) On Fri, Sep 30, 2011 at 1:41 PM, Karen Eilbeck <kei...@ge... <http://kei...@ge...> > wrote: Hi Kevin I think that the mods use CDS as a split feature. So the total CDS of a transcript will have a start and stop, but the feature is across several lines of GFF3. I could be wrong though... --Karen On 9/28/11 3:07 AM, "Kevin Howe" <kev...@wo... <http://kev...@wo...> <http://kev...@wo...> > wrote: Hi, The definition of the "CDS" SO term states: "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." Is this rather strict definition intentional? In the GFF3 specification, "CDS" is used to define an exonic region that is coding across its whole length (with population of the phase field compulsory).This usage is consistent with the majority of GFF3s I have come across. Many (most) of these features will not start/end with start/stop coons. So...is the definition of the term overly specific? Or are people using the term in an inappropriate context? Many thanks, Kevin Howe ------------------------------------------------------------------------------ All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2 _______________________________________________ SOng-devel mailing list SOn...@li... <http://SOn...@li...> https://lists.sourceforge.net/lists/listinfo/song-devel ------------------------------------------------------------------------------ All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2 _______________________________________________ SOng-devel mailing list SOn...@li... https://lists.sourceforge.net/lists/listinfo/song-devel |