Hi, I have gone through the Biostars web page. I could not find the answer for my question. I am trying to convert 2000 gene descriptions (full name of genes) to gene symbols (acronyms). As I am working with a non-model species, Gene ID did not help much. I also tried bioDBnet and David. But not much help either. Is there any other online or offline tools I can use? thanks in advance.
You could use NCBI unix utilities. With the example you posted above (assuming you are working with Atlantic Salmon:
$ esearch -db gene -query "sulfatase 1 [TITLE] AND Salmo salar [ORGN]" | esummary | grep -w "Name" <Name>sulf1</Name> $ esearch -db gene -query "monooxygenase [TITLE] AND Salmo salar [ORGN]" | esummary | grep -w "Name" <Name>ywhaz</Name> <Name>coq6</Name> <Name>ywhah</Name> <Name>fmo5</Name> <Name>moxd1</Name> <Name>agmo</Name> <Name>coq6</Name> <Name>msmo1</Name> <Name>pam</Name> <Name>bcmo1</Name>
As long as the titles you have are specific they should result in a single name. Otherwise you may get more than one gene (example #2 above).
Hello, in your shoes I probably would:
a) retrieve all NCBI sequences for your taxon in GenBank format
b) search for each gene description in your GenBank database (e.g. in the "Official Full Name" field)
c) fetch the corresponding gene symbol (i.e. in the "Official Symbol" field)
Hope this helps!