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Missing acorn worm genome data
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14 months ago
cdsouthan ♦ 1.8k

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 coveing 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 thier assemblies to Ensembl gene builds? That would give the rest of us the chance to do our own comparisons

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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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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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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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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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