Hello,
If I were to now re-annotate C. elegans and briggsae what tools would I use, to yield best accuracy? Knowing the in the early annotation of these organism de novo techniques were used. Would I change those techniques in any way?
thanks!
edit: basically I’m wondering how would you annotate protein coding genes in C. elegans and C. briggsae with the best accuracy?
I noticed a lot of you viewed the thread but didn’t reply was it because I didn’t word this properly?
Hmm…not sure I understand what you are asking here. Is this a hypothetical question for a project/exam or is there a specific reason that you would want to ‘re-annotate’ what is already annotated?
The annotation process and associated tools used are already described within the pages of wormbase and in references listed therein;
http://en.wikipedia.org/wiki/WormBase
If this is not what you meant, then perhaps you could rephrase your question?
Steve
The problem of your question, that the “most accurate way to curate genes” is always dependent on the point in time you ask the question, as additional data/experiments and tools become available.
If we would have the current knowledge when we started making C.elegans genes, we might have done it differently, but with the then knowledge it was deemed to be the best way.
The main “problem” is that C.elegans scientists are quite productive, so your “correct gene model” might potentially change every other month, because someone published some new insights.
But the classic way, is:
pick a geneset you believe is correct and then optimise your annotation process on it … well knowing that “correct” will change over time. Have a look at some gene prediction paper, they explain the optimisation process quite well (as they usually at the very least compare Sensitivity/Specificity on bp / splice-site / transcript level).