Question: taxonomy download from NCBI based on geneID
0
gravatar for nabiyogesh
4 months ago by
nabiyogesh0
nabiyogesh0 wrote:

Is it possible to download taxonomy based on gene Id for a large dataset from NCBI using biomartr package?

vi arsM.ID.txt

AAAK03000116.1
AAAL02000001.1
AACD01000079.1
AACS02000002.1
AADV02000002.1
AADV02000014.1
AADV02000142.1
AADV02000157.1
AADV02000160.1
AADV02000163.1
AAEK01000011.1
AAEK01000037.1
AAEW02000007.1
AAEW02000015.1
AAEW02000015.1

taxonomy format should be like below:

I need taxonomy in this format:

AM774418.1 Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Halobacterium  Halobacterium salinarum R1
LOPV01000533.1 Archaea; Euryarchaeota; Halobacteria; Haloferacales; Haloferacaceae; Haloferax  Haloferax sp. SB29
CP003125.1      Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Geobacillus; Geobacillus thermoleovorans group  Geobacillus 
BAWP01000033.1  Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Parageobacillus Parageobacillus thermoglucosidasius NBRC 
MEFJ01000016.1  Bacteria; Proteobacteria; Betaproteobacteria; Nitrosomonadales; Thiobacillaceae; Thiobacillus   Thiobacillus sp. SCN 
FXAE01000009.1  Bacteria; Firmicutes; Bacilli; Bacillales; Paenibacillaceae; Paenibacillus      Paenibacillus barengoltzii J12
biomartr bioconducter • 84 views
ADD COMMENTlink written 4 months ago by nabiyogesh0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 339 users visited in the last hour