2 replies to this topic

[prabhubct]

How to find all Microarray expression probes for Whole genome of Bacteria ( e.g. Salmonella) at once. How to upload all genes of salmonella and find probes for them, I tried in Agilent Earray. usingftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Salmonella_enterica_serovar_Typhimurium_LT2_uid57799/NC_003197.ffn;type=a

this link. I got all genes in same FASTA file format. But Agilent recognized probes only for 97 targets ( 10 probes per target) out of 4423 targets. How I am supposed to get probes information for all target genes at once?
Any other method of finding micro-array expression probes iwill also be useful.

[toejam]

hey prab,

I believe ncbi allows up and downloading of data via command line, if you're using linux. It's been a while since I did it (over 5 years ago now) but it should still be available, you need to connect via FTP to their website. I guess if you google "NCBI FTP command line data download" you can get pretty close to what you're after.

cheers.

tj.

[prabhubct]

Hi Tj,
   I will try as you suggested. thnaks.