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CDS and Proteins and ncRNAs are predicted from all these datasets.
For download from the publication page - we ONLY provide these Genbank-derived
datasets AND user-provided annotated data (if any), and other custom datasets provided
by the authors
Annotation
• All reads available (either via Genbank or the Trace Archive) that are longer than 250bp
on avg should be annotated - How well does the pipeline work for such short seqs? How
well does it work for Sanger seqs for that matter? What is the relative utility ? What to do
with ESTs? GSS?
• If annotation is available in Genbank, it should be retrieved and discussed - not available,
one exception is Leptospirillum assemly from AMD - 8 genome scaffold sequences with
predicted proteins have been deposited as a separate project from the metagenomic
projects.
• If an environmental dataset has scaffolds for organisms deposited in Genbank, should we
treat it like an organism? LIke an environmental set? As an environmnental set I think.
Depends on whether this data makes it into Genbank NR (and hence CAMERA nIAA) or not.
• Can we annotate contigs/scaffolds via our metagenomic annotation pipeline? Or should
we be using the prok pipeline?
• Which predicted proteins should be included in clusters?
Blastable Datasets
• reads should be added to All Metagenomic reads, same for ORFs, Peptides, ncRNAs
• Contigs and assemblies should be added to "All Metagenomic Assemblies" , no such db
presently since GOS is the only one with assemblies, when/if we DO provide this, it
should only contain "site-specific" assemblies.
• If available, mapping between reads and contigs should be absorbed
New datsets:
Only one new (CAMERA-relevant-maybe) project is available for update: Termite gut
metagenome - No traces deposited , data is 1337 fosmid clone seqs, and 1 WGS
entry (55,108 contigs) and 48 glycoside hydrolase family genes. Contacted JGI about
the
traces. http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Ove
rview&list_uids=19107?