How To Search Blast With Ensg Id'S?

Question

[Asmaa]

I have some ENSG id's and I would like to search BLAST database with this id's. When I use the ENSG id's directly, BLAST cannot find any genes. I think I need to convert the ENSG id's to some other format so I can search the database.

I appreciate if you can suggest me which format I should convert or is there a way to convert this ENSG to a suitable format.

[Neilfws]

Which organism are the ENSG from?

[Neilfws]

Which organism are the ENSG from? And how are you running BLAST? Are you trying to paste IDs into the BLAST query form at NCBI?

[Asmaa]

the organism is human and i am using BLAST via command line. but when i give ensg id's to the command line, it cannot find anything. so i thought i should convert this id's first, and then give the command line the correct type of id. but i searched internet, i couldn't find which format i should convert to..

[Neilfws]

Then I assume you are using BLAST+, which allows a list of identifiers as input? The identifiers you need are called GIs and are specific to NCBI/Entrez.

[Asmaa]

Thanks a lot for you answer. I did what you suggested and it work for small subset of my data. However, i have 97480 ENSG id's and i want to convert them to Entrez Gene Id. As this file is very big ; it took a lot of time and it has not been done even after 20 hours. I would deeply appreciate if you could let me know what i can do for this big file.

Answer 1

[Biojl]

You can use Biomart to convert your ENSEMBL ID's to another format.

http://www.ensembl.org/biomart/martview

Just select your species, use your list od ID's as a filter and navigate through attributes. You can select Associated Gene Name for the generic name of the gene or search in Features>External>External references for the format you need. Check which ones your blast version can use (web version, command line, etc).

[Neilfws]

I don't believe that BioMart will convert directly from Ensembl Gene to NCBI GI.

[Biojl]

I think you're wrong, since biomart has the pubmed ID option and pubmed belongs to ncbi...

[Bert Overduin]

BioMart has only the Genbank accession numbers, not the GI numbers. PubMed has nothing to do with this ....