sequence annotation for gene name or gene symbol

Question

[Kurban]

Hey guys,

I have a few rookie questions. I have a several hundreds of transcripts which are up regulated in an insect response to low temperature. I wanna use DAVID to analyse them.

But when I looked at DAVID, it receives genes in list of their ENTREZ_ID and OFFICIAL_GENE_SYMBOL (I assume gene symbol refers to gene name right?). I have annotated those sequences by using blast2go before, but the software gives the sequence's description, not gene name or seq ID.

So what I wanna ask here is how can I get my sequence corresponding ENTREZ ID, gene symbol (name) or any information like that from database like NCBI.

I thought may be I could get those information from blasting my sequences with NCBI nr.fasta data, but when I see that the whole file in NCBI the compressed version of the file is around 14G, then I think I can not do that on laptop, do I?

Could you please give me some tips on those, which could really help me with the downstream analysis of those sequences.

Answer 1

[Jean-Karim Heriche]

The gene symbol is a short form of the gene name e.g. PLK1 is the gene symbol for human gene name polo-like kinase 1. To convert between identifiers, you can use a BioMart service having your species of interest.