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#654 identify missing sno's/ training?
1. Get a list of snos in S. cerevise
2. check which are missing in fission yeast
3. How many of these are in introns?
4. Are they in introns in the corresponding fisison yeast genes
5. Are they in Rfam? if not submit
6. Can they be identifed from Pfam signature
7. Go back to Todds method, can this be implorved?
snR18 YAL003W check tef5
ssnR44 missing YLR367E pomb gene does not have intron.
snR59 missing YPL198w check rpl701,2,3
snR52 not in an intron, pol III transcribed, missing
SPNCRNA.497 is in rps3 intron, could it be a sono?
I also noticed that the sno/snu's in PomBase are all noted as "known"
Maybe we need to use the same "status" qualifiers for these so we can keep track of which are predicted/published (or maybe this could be inferred from evidence codes?).
Will become increasingly important to know which of the ~1500 ncRNAs are characterised.....
1 (& 3). http://www.yeastgenome.org/snoRNAtable.shtml
might be useful http://lowelab.ucsc.edu/databases.html
Well, I'm pretty sure I haven't located ALL of these.
So I guess
Step 1 if to find which ones are missing in FY
Step 2, see if any of these are easily identifiable by Blasting S.c sequences against pombe genome (if any of Sam's transcripts are in the hit list that's probably a true positive.....
Step 3 We can search Sam's transcripts against Rfam...he has already done this but we could repeat with a low threshold to see if we turn up any candidates
Step 4 Is there any other info we could use. Some sno's are in introns, and I think this location might be conserved for some sno's see SPNCRNA.497 above
Step 5 If we don't have any success we could contact an expert like Todd Lowe who helped to identify the original ones which we couldn't detect by Blast, computationally.
Step 6 refine sno feature annotations using SO terms
Step 7 Make inferences for GO processed and modifications (need to decide on/establish system for
RNA modifications)
Step 8 Would a table like SGDs be useful (or can we generate one from a query once all the annotations are made?)
Step 9 (Other stuff which I have likely not though about)
Actually I didn't know Todd had a server, This might be the best for the first pass.
We could transfer this to a potential student project combined with other analysis of ncRNAs (not also 'special RNAs in Sam's paper might be sno's)
Ticket moved from /p/pombase/sequence-analysis/31/
Can't be converted: