Question: GenBank accesion number to gene id
1
gravatar for trumbia
8 weeks 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 • 223 views
ADD COMMENTlink modified 8 weeks ago by piyushjo170 • written 8 weeks 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 8 weeks ago by genomax73k

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 8 weeks 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 8 weeks ago by genomax73k

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 8 weeks ago by trumbia10

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

ADD REPLYlink written 8 weeks ago by piyushjo170
0
gravatar for Viz
8 weeks 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 8 weeks 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 8 weeks ago by trumbia10
0
gravatar for piyushjo
8 weeks ago by
piyushjo170
piyushjo170 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 8 weeks ago by piyushjo170

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

ADD REPLYlink written 8 weeks 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 8 weeks ago by piyushjo170

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

ADD REPLYlink written 8 weeks ago by trumbia10
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