Missing acorn worm genome data

The Acorn Worm genomes just written up in Nature are not easy to search.

http://www.nature.com/nature/journal/v527/n7579/full/nature16150.html

Saccoglossus kowalevskii does have GeneBank entries covering the genome

http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=10224

but Ptychodera flava does not

http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=63121

It appears to be DDBJ only at the moment

http://trace.ddbj.nig.ac.jp/BPSearch/bioproject?acc=PRJDB3182

Any chance Emily_Ensembl the authors could be prevailed upon to submit their assemblies to Ensembl gene builds? That would give the rest of us the chance to do our own comparisons

acorn-worm ensembl

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updated 4.1 years ago by Ram

• written 10.7 years ago by cdsouthan

Is this one of those projects that was published after a long time even though the sequencing was done by Baylor back in late 2000's?

What is this assembly table referring to: ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000003605.2.assembly.txt?

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written 10.7 years ago by GenoMax

Yes and I found the Saccoglossus kowalevskii data that was also actually BLAST indexed

http://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA12887

But the Ptychodera flava is not search indexed at DDBJ

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updated 6.7 years ago by Ram

• written 10.7 years ago by cdsouthan

It should be easy enough to make the index yourself. Data was released here for Ptychodera flava: http://www.ddbj.nig.ac.jp/whatsnew/wn151124-e.html

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updated 6.7 years ago by Ram

• written 10.7 years ago by GenoMax

I know but its not part of my day job - has anyone done this? and could they fix the major deletion in the ORF below? (e.g. with transcript data)

>PFL3_pfl_40v0_9_20150316_1g4029.t1
MRKARSVVNRSQNLNRVPLSPTTEEPSTENNLRGKPGQGYYIELSMGAPPQSVNVLVDTG
SSNFAVASAPHPFIARYFNTDKSSTYINSGIAVDVPYTQGRWDGYLGTDLVALSAISNVT
ARVNIASITKSENFFINGSNWEGILGLAYDEIARPDSSLTPFFDSYASQTAIDDIFTLQL
CGSTDKVDSSELGGTMYNFDKTIVDSGTTNFRVPVKVFDALVHAIDDATPVEVSPEFYTG
TELMCWSDDTTPWEHFPSVKISLLAEDSSQSFKLLISPKQYMRKVDDGTSEADDCYKFAI
TTSSSGSVIGAVIMEGFYVIFDRHNKRIGFAASTCADNSTGCAYEVPESNETTLMAVAYA
MASICAICMLPLLVMLFQCYRKGSKEKKYGCDSENLVHQ

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updated 6.7 years ago by Ram

• written 10.7 years ago by cdsouthan

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