NOV 11 2010

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Contents

Next release 2.19 (Dec. 17th)

Migrating reference tables and GO to Chado
  • Migrate the batch reference update script. [Done]

[Working on]

  • Migrate the dicty reference page to new code and test it.
  • Migrate the reference search.
Interpro domains for all dicty genes (Yulia)
We store both domains that are integrated into InterPRO and are unintegrated (i.e. TMHMM and SignalP domains are not integrated). Some signatures reported in InterProScan are marked as unintegrated but still have valuable information that should be stored and made searchable..
problem encountered: signature names seem to change qrequently. Waiting for responce from Interpro with explanations (expected behavior is to have stable data in between InterPro releases)
Automate curation stats -Excel (Yulia)
Link to ENSEMBL
Our links from the genome browse don't work anymore (at least for me - Petra), e.g. [1]. And it would be nice to link to the EnsemblProtists from our gene pages. Example link, [2]

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 (Yulia) [Done]
Pseudogene features cannot be associated with another gene, which needs fixing. See issue [3] [Petra]
Link outs to GenBank (Yulia) [Done]

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?
Stock Center User requests (Yulia) [Done]
  • Add shopping cart to each strain and plasmid page.
    • SC search pages
    • strain catalog
    • strain page
  • Make shopping cart 'sticky' so it remembers what's in it. Action: extended cookies lifespan to 3 month (was set to expire with session end)


Expression Data from Harry

  • Harry sent expression, spatial and temporal, plus cell cycle regulation data, in an Excel sheet with Macros. User request
  • We should have a look at the data table and make a plan when and how we can use it.
  • I can visualize the graphs (not so elegantly because I can't have Macros on the Mac) and it would be great to have those linked to genes. Here is a screenshot of what the graphs look like Image:Harry_graphs.png

Update on MAKER ?

  • Quest would be suitable for this job [Talk to dong about it]
    • However need to do a test run on avery(suggested by dong also)
  • FYI: cross_match software and repeatmasker database has to be obtained after e-mail registration (takes at least a week to happen)
  • Overall: Including setup estimated 7 days for the first batch of runs


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


On 9/28/10 4:50 PM, Samuel Kerrien wrote:

Brilliant, do get in touch again if we can help further.
Cheers

Sam

On 28 September 2010 15:09, Pascale Gaudet <pgaudet@northwestern.edu> wrote:

Dear Sam,
I can't find a reply to this email - but I wanted to let you know we have discussed 
the UniProt export files and we can use them to integrate the IntAct data into dictyBase.
Best regards,

Pascale
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