SEPT 27 2010

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AX4 sequence variations from Gareth

We got Kuspa AX4 sequence variations from Gareth in the format samtools pileup [1]. He sent the filtered file, with positions, the kind of changes, consensus, SNP, and mapping quality, depth. We need to work together to make this useful for us curators, and ultimately this should help enormously for a large genome update [Petra]

  • We could use galaxy tool to filter the pileup file, get exact chromosomal location of variants(indel/SNPs). -sidd

Action item: Generate list of not yet curated genes having sequence variations [Sidd]

Separating floatigs

Do we still have plans to do that? Maybe independent of that, I found a short contig in the 2F concatemer (DDB0215024), that's for sure a duplicate of an integrated chr 2 region. There were 4 genes on the contig of which two were tiny I deleted those, DDB_G0294182 (7 aa), DDB_G0294184 (21 aa - conserved piece occuring in 7 genes on chr 2,3 and 5). Then there are two genes that are predicted exactly like on chr2: DDB_G0271418/DDB_G0294188 and DDB_G0271416/DDB_G0294186. I blasted the genomic sequence and there are 7 mismatches, mostly at the ends of the small 2F contig, but I definitely think these are redundant. [Petra]

IntAct

Intact- Uniprot export files

  • We need to get back to Sam and Sandra about whether we're able to import their data.
  • The reason to do this (even though our SAB was not too interested) is that GO is thinking to replace 'protein binding' annotations by those from the interaction databases, so we should make sure Dicty is included.
  • What do we want to store, display and search? [Yulia]

Email from Eva Huala

Need to follow up. E-mail response sent by Eric and Sidd, Sept. 23rd [2]

RATT

Pascale: I'd like to know if that tool would be helpful for us to update genome versions: [3]

  • It does transfer of annotations and uses Mummer as a backend. -sidd

Attribution of annotations

  • (pascale) At the Dicty meeting I presented about 'Community involvement in annotation', and the response was rather positive (we have even received a few inquiries). One important issue is that we should emphasize the annotations provided by users. Right now this is not shown anywhere, and of course that makes it much less attractive for people to submit their data.
  • (Petra) We have a link on test to a new User_Annotations User annotation wiki. The idea is that people add themselves to the wiki.

Action: Warren is going to look at the submission form

  • Email sent to contributers to comment on what's on test [Sept. 27, Petra]

Link outs to GenBank

The GenBank links on the Gene pages (see for example sadA gene) we link out to our own version of the sequence (for example sadA AY178767). This is misleading and also unnecessary. We should link to GenBank directly and remove the tab for the GenBank sequence.

  • Do we keep GenBank sequences in BLAST options? If so do we link out to GenBank as well? [Yulia]
  • GBrowse linkouts [Yulia]

Stock Center items (from Dicty meeting)

    • Charge for strains, suggested $10-20.-. encouraged by people at the meeting to prevent "abuse". Action: Talk to Matt!
    • Can the Stock Center become the american distributor for Formedium HL5? As such we get a 25 % discount and could pay for shipping? But needs accounting, should be seen in conjunction with charging for strains and needs to be discussed with NIH. Action: Talk to Matt.

Stock Center User requests

  • Add shopping cart to each strain and plasmid page.
    • As of now there is one on plasmid page/plasmid catalog page but not on strain page/strain catalog page [Yulia]
  • Make shopping cart 'sticky' so it remembers what's in it (cookies?). Action: ?

Next release 2.19

Migrating reference tables and GO to Chado

Migrating gene-publication links from SGD -> Chado. [Done]

[Working on]

  • Migrate the dicty reference page to new code and test it.
  • Migrate the batch reference update script.
Interpro domains for all dicty genes (Yulia)
Running interpro analysis using InterProScan web service instead of relying on interpro-uniprot-dictybase mapping)
Link to ENSEMBL
Our links from the genome browse don't work anymore (at least for me - Petra), e.g. [4]. And it would be nice to link to the EnsemblProtists from our gene pages. Example link, [5]

working link for EmsemblProtists for GBrowse http://protists.ensembl.org/Dictyostelium_discoideum/Location/View?db=core;r=1:1000-30000

Fix Pseudogene - Gene association bug
Pseudogene features cannot be associated with another gene, which needs fixing. See issue [6] [Petra]
Automate curation stats -Excel (Yulia)

Comments on MAKER

  • A local installation of MAKER interface for web based submission is doable. It comes with the software itself.
  • Integrating Gene id in MAKDER pipeline is possible provided we get its output as GFF3.
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