I have seen this post that allows gene conversion from RefSeq IDs to gene names. What I would like is a tool (command line or web-based) that:
- takes as input a list of gene names (shortcut name or comprehensive gene name) AND a query species
- outputs the list of RefSeq IDs
In my case
- the species would be Stegastes partitus
the gene names
LOC103370819 prtfdc1 LOC103367872 tfec colony stimulating factor 1 receptor (csf1r)
I first thought of using
blastdbcmd but it seems that
blastdbcmd does not take gene names as input.
$blastdbcmd -db nt_Spar -dbtype nucl -entry prtfdc1 #nt_Spar a subset of nt with only S. partitus sequences Error: prtfdc1: OID not found
I have tried using Batch Entrez but it does not accept gene names as input neither.
Many thanks for your help!