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Many of the bacterial genomes have multiple contigs or chromosomes. The sorting needs to be on the contig, and on the start site. Brucella has 2 chromosomes and look at how this looks-
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When users take the effort to select RefSeq as their annotation choice:
Why does the table return PATRIC results?
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Brucella PF tab, applied keyword filters to see membrane proteins. Filtered families are shown
correctly in table and heatmap.
Then, I reset the filters, to show all families. They are correctly di…
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example: Brucella / Brucella abortus
https://www.alpha.patricbrc.org/view/Taxonomy/118882
There are many taxonomy nodes with genomes labeled as "no rank", which are not displayed as subtree.
Howev…
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The data API for FNA is missing one base every 60 characters. Please see the comparison example below. The bases on the red line are the delta between the two. This bug may be contributing to the "too…
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It seems that the global search is currently searching only for CDSs in genome features.
So, if I search for Brucella rRNA, I don't actually get rRNAs. If I click on genome features, it takes me to a…
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I"m wondering why there is such a huge difference (or should I say "yuge" between what I see at GEO for Brucella, and what appears in PATRIC. At GEO it says there are 547 datasets. PATRIC says 45.
H…
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Total length of the assembly would be good to know again to compare with total length of assemblies generated from other assemblers.
Please add to makesummary output
Thanks.
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@rdmpage suggested to add Wardeh, M. et al., 2015. Database of host-pathogen and related species interactions, and their global distribution. Sci. Data, 2, p.150049. Available at: http://dx.doi.org/10…
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Once in the beginning:
- [x] genome lengths stats
- [x] sequences: only number and total length
- [x] stats for numbers of chromosomes in genomes
After each iteration:
- [x] print "Iteration $i"
- [x…