I've manage to build a LSU database with the commands for the SSU, but I "don't" like the analyses results with the silva phylogeny, specifically with the classification given for the
since it does not discriminate chloroplasts origin.
I blasted one sequence classified as chloroplast in NCBI and it provided me with a different annotation that I would like to persue. all hits belonged to the same order, so I could have my chloroplasts classified at least at that level...
Eukaryota; Viridiplantae; Chlorophyta; Trebouxiophyceae; Chlorellales
Nannochloris normandinae 90% JQ921007.1
'Chlorella' mirabilis culture-collection SAG:38.88 chloroplast,90% KM462865.1
Parachlorella kessleri culture-collection SAG:211-11g chloroplast, complete genome 90% FJ968741.1
Coccobotrys verrucariae strain SAG 16.97 23S 89% JQ921003.1
So my question is,
How can I use the NCBI classification to annotate the LSU data set that I have?
We have access to a map file
https://www.arb-silva.de/no_cache/downl ... 132.txt.gz
Is it possible to link to the sequences of the arb LSU file to the NCBI annotation?. Is it possible?
Maybe on the
make this part
is genbank phylogeny identical to NCBI ??
Thank you for any help, I would very much appreciate that
It would be totally killer if mothur could...
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Last edited by itiago on Thu Jan 11, 2018 10:29 am, edited 2 times in total.
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