Using Bioconductor Biomart to find gene name for sseqid from blastn results

Question

[jannetta.steyn]

Hi All

I need to find a gene name using the sseqid from blastn results: gi|19698730|gb|AC079789.7|

and I want to use the gi or gb id to find a gene name. I have parsed my data into an R dataframe where sseqid1 contains gi and sseqid2 contains gb.

This is my R code:

ensembl <- useMart('ENSEMBL_MART_ENSEMBL', 
                   dataset="cporcellus_gene_ensembl")
keys=as.character(res$sseqid1)
res$genename = getBM(
                   attributes=c('external_gene_name','protein_id',
                   'refseq_mrna_predicted','entrezgene'),
                   values=keys,mart=ensembl)

The last statement results in an error because of the biomart result set. My guess is that it returns more than one result per gi but I can't really figure out what biomart is doing, why it is doing it and what I need to do to fix it.

What I want is a gene name for each sseqid. I don't care whether the gi or the gb is used. I can't find exact definitions for the abbreviations gi and gb and I haven't been able to find out which of the biomart attributes these relate to to. If this information is in the documentation, I have not been able to find it.

Is there anyone that can help me out to get this done?

Thanks in advance. Jannetta