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.
1 answer
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).
BioMart has only the Genbank accession numbers, not the GI numbers. PubMed has nothing to do with this ....
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Which organism are the ENSG from?
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?
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..
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.
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.