Extract dna sequences from given ids using R codes/package

Question

[MAPK]

I don't remember exactly what I had used in the past, but I might have used biomart or rentrez to extract DNA sequences using NCBI gene IDs. What are the tools in R package to extract fasta sequences with NCBI seq IDs? Thanks

Answer 1

[Jean-Karim Heriche]

Both biomaRt and rentrez should do the job, the difference is that one will give you Ensembl sequences, the other NCBI ones. Check the rentrez tutorial here. There's also the reutils package.

[MAPK]

How do you convert gene symbols to UID which is required to extract genes using reutils?

[Jean-Karim Heriche]

Something like the following should give you the list of IDs that match the symbol:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=AURKB[Gene+Name]+AND+human[Organism]

You can also use BioMart for ID conversion.