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PomBase curation
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document procedure for Sequence and feature updates #633

Open pombase-admin opened 15 years ago

pombase-admin commented 15 years ago

  1. Add new telomeric region to contigs (are there 2 now?)

  2. Do fixes small which are confirmed http://www.sanger.ac.uk/Projects/S\_pombe/sequence\_updates.shtml http://www.sanger.ac.uk/Projects/S\_pombe/sequence\_discrepancies.shtml

  3. Can we fill any gaps using Broad data? Speak to Nick Rhind

To Do Give community advance notice of contig changes Make Fixes Update Stats/ webpage (sequencing status etc)/ download data EMBL resubmission

Original comment by: ValWood

pombase-admin commented 15 years ago

Original comment by: ValWood

pombase-admin commented 15 years ago

The gap-filling sequence on the left arm of chromosome 2 in fission yeast Schizosaccharomyces pombe Yeast Volume 25, Issue 9, Date: September 2008, Pages: 673-679 Mayumi Sasaki, Alimjan Idiris, Aya Tada, Hiromichi Kumagai, Yuko Giga-Hama, Hideki Tohda

was there another gap filling sequence?

Original comment by: ValWood

pombase-admin commented 14 years ago

Include i) all frameshifts/ sequence errors recorded ii) versioning 27D7 repeat

Original comment by: ValWood

ValWood commented 8 years ago

notes transferred from issues/27

• Hideki, gap filling ? • Sasaki M, Idiris A, Tada A, Kumagai H, Giga-Hama Y, Tohda H. Yeast. 2008 Sep;25(9):673-9.PMID: 18727152 new telomeric clone pending http://www.sanger.ac.uk/Projects/S\_pombe/sequence\_updates.shtml http://www.sanger.ac.uk/Projects/S\_pombe/sequence\_discrepancies.shtml

from trac ticket: https://sourceforge.net/apps/trac/pombase/ticket/30

ValWood commented 8 years ago

read in UTR files to ensure sequence updates propagated

ValWood commented 8 years ago

This is in PMID: 24929437 should already be in be in the main changes

We detected translation of the C terminal part of the Nup184 protein, which was not predicted to be translated in S. pombe due to an in-frame stop codon created by a single nucleotide deletion32. Translation of this region in the strains we used was explained by the presence of single nucleotide insertion that reverted the effect of the deletion in the reference sequence (Supplementary Fig. 5A and 5B).

mah11 commented 8 years ago

From https://www.ebi.ac.uk/panda/jira/browse/PB-507:

Make sure AB325691 contig gets incorporated into chromosome 2.

(Full text of ticket description: "This small contig appears as chromosome AB325691 http://www.pombase.org/spombe/result/SPBC460.05 it is actually a small chromosome 2 contig (left end I think) How easy is it to add a chromosome 2 assignment (in the next assembly this will be built into the chromosome so I have put this at low priority)")

ValWood commented 8 years ago

The sequence updates will need to be low priority. They won't be able to happen until we have a 'lift over' equivalent ...world of pain...

ValWood commented 8 years ago

Very partial list in random order:

High priority datasets to host for refining gene structures: Lantermann data hosted https://github.com/pombase/website/issues/62 Dutrow https://github.com/pombase/website/issues/63 CAGE data? (Olaf) https://github.com/pombase/website/issues/368

Other tasks for after sequence changes: Fixing alleles in genes where sequence has changed Remapping existing datasets with lift-over Update EMBL files -> RNA central check Folder on desk top check Folder in e-mail check Open tickets. check actions from planning meeting Agenda

Identified sources of sequence revisions Make revisions to sequence proposed by broad and confirmed by Li-Lin DU and ??? Revise gene structures accordingly Merge in telomeric contig revise UTRS and non coding RNA structures etc Issues

What to do about mating type region fo reference strain What to do about mozaic nature of sequence (problems for EMBL submission) Making and EMBL dump, ensuring the RNAs and Protein info required by UniProt? and RNA central is present etc planning to synchronise with EG

from https://github.com/pombase/curation/issues/903

ValWood commented 7 years ago

https://github.com/pombase/website/issues/48

ValWood commented 6 years ago

also a list of SNPs from Megan Behringer, I put Ys in who identified them first. The Y’s in the Broad column are all the mutations shared between my two isolates that were first identified as errors by the broad. Then the second column are errors not identified by Broad but identified by Hu et al. The third column are SNPS not previously reported by Broad or Hu et al, and are newly identified in our study.

"mutation accumulation study in S. pombe (Behringer and Hall, 2016) and am currently finishing up a review article comparing mutation results in our study and a study by Farlow et al (2015). In comparing the ancestors used in both our studies, not only did I identify 171 differences shared in our ancestors that were present in the list of 190 discrepancies from the Broad sequence reported on your 'Sequence Updates Pending' page. I also identified an additional 36 differences shared in our ancestors that were not included in your list. Since the other study was done in an H+ line and our study was performed using 972 h-"