converting accession numbers to Gene Symbol

Question

[R]

hello everyone:

I have a file including different accession numbers and i want to convert them into the "Gene symbols". i wonder if anyone could help me by telling me " a code of R" or " Database"

a part of my accession numbers are like below:

Q84X92_HORVD;
A2WZ82_ORYSA;
A2YGW3_ORYSA;
NP_001049423.1;
NP_001049301.1;
NP_001058077.1;
NP_001046629.1;
A2YBX9_ORYSA;
NP_001053139.1;
A2ZEJ1_ORYSA;
A2Z234_ORYSA;
NP_001063728.1;
RS12_HORVU;
NP_001051718.1;
NP_001047741.1;
NP_001067361.1;
NP_001065747.1;

[Jean-Karim Heriche]

You seem to have a mixture of ID types (e.g. Q84X92_HORVD is from UniProt, NP_001049423.1 is from RefSeq) from different organisms. The way I've dealt with this situation was to write a perl script using the Ensembl API (assuming species are represented in Ensembl)

You could use BioMart either from a web site or from the biomaRt R package but then you may have to go one species at a time.

EDIT: You may want to remove the version number (i.e. the dot and the following digit e.g. .1) as some tools may not recognize it.

Answer 1

[Buffo]

BioDBnet is the most easy way :)

[Jean-Karim Heriche]

It doesn't seem to be able to deal with IDs from multiple species, one needs to go one species at a time.