How to build a Silva LSU V132 with NCBI annotation

It would be totally killer if mothur could...
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itiago
Posts: 7
Joined: Tue Nov 24, 2015 3:56 am

How to build a Silva LSU V132 with NCBI annotation

Post by itiago » Wed Jan 10, 2018 1:01 pm

Hi
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
Bacteria;Cyanobacteria;Oxyphotobacteria;Chloroplast;Chloroplast_fa;Chloroplast_ge;

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?

or...
Maybe on the

SUFFIX fasta
BEGIN
>*(acc).*(name)\t*(align_ident_slv)\t*(tax_slv);
*(|export_sequence)

make this part

>*(acc).*(name)\t*(align_ident_slv)\t*(tax_genbank);

is genbank phylogeny identical to NCBI ??

Thank you for any help, I would very much appreciate that
Best
Igor
Last edited by itiago on Thu Jan 11, 2018 10:29 am, edited 2 times in total.

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