Question: GenBank accesion number to gene id
1
gravatar for trumbia
13 months ago by
trumbia10
trumbia10 wrote:

I have list of genbank accesion id that start with EOT and I want to convert them to ensemblgene id. I am really sturuggling with this. Can you help me? https://www.ncbi.nlm.nih.gov/protein/EOT21827.1/ ps: i work with Pseudomonas aeruginosa PA14

rna-seq • 729 views
ADD COMMENTlink modified 13 months ago by piyushjo520 • written 13 months ago by trumbia10

I am not sure why you need ensemblgene ID's but a straight conversion may not be available. You may need to blast your proteins against ensembl version of this genome to get the info you need.

ADD REPLYlink written 13 months ago by genomax89k

I have DESeq2 Result so that I do not name of the protein by one by. I can not check all of them cause there are 5000 of them. I need to convert them since my model has ensembl ids.

ADD REPLYlink written 13 months ago by trumbia10

What model are you referring to? Perhaps you could just do recounting with ensembl GFF and get the ID's you need?

ADD REPLYlink written 13 months ago by genomax89k

I got my model from agora which is pseudomonas areuginas and but the gene id in that model is different from my deseq result.

ADD REPLYlink written 13 months ago by trumbia10

Could list at least 5 examples of genbank and other gene id you are referring to?

ADD REPLYlink written 13 months ago by piyushjo520
0
gravatar for Viz
13 months ago by
Viz40
Viz40 wrote:

bioDBnet has a "DB to DB" function that allows the interchanging of any two standard gene name formats

https://biodbnet-abcc.ncifcrf.gov/db/db2db.php

Just enter your gene names as the Genbank input and select whatever output format you want

ADD COMMENTlink written 13 months ago by Viz40

Hey, I chose the option of GenBank Protein Accesion and it did not give any result. Did I do smth wrong?

ADD REPLYlink written 13 months ago by trumbia10
0
gravatar for piyushjo
13 months ago by
piyushjo520
piyushjo520 wrote:

Biomart from ensembl.org has such features. You can convert any given id to another id. I see the you organism has an ensembl page. I think you could use the biomaRt package in R and follow the example for human data from below vignette.

https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/biomaRt.html

ADD COMMENTlink written 13 months ago by piyushjo520

The problem is biomart does not have any library about bacteria or should I use another thing?

ADD REPLYlink written 13 months ago by trumbia10

Yes, sorry. It looks like while ensembl has a page your organism it doesn't show up in the biomart. http://bacteria.ensembl.org/Pseudomonas_aeruginosa_pa14/Info/Index

ADD REPLYlink written 13 months ago by piyushjo520

Yes I know this page but the annotation is different. I wanted to convert it.

ADD REPLYlink written 13 months ago by trumbia10
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