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
2 answers
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
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
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
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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.
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.
What model are you referring to? Perhaps you could just do recounting with ensembl GFF and get the ID's you need?
I got my model from agora which is pseudomonas areuginas and but the gene id in that model is different from my deseq result.
Could list at least 5 examples of genbank and other gene id you are referring to?