Jump to content

  • Log in with Facebook Log in with Twitter Log in with Windows Live Log In with Google      Sign In   
  • Create Account

Submit your paper to J Biol Methods today!
Photo
- - - - -

How to find all Microarray expression probes for Whole genome of Bacteria ( e.g.

Microarray Bacteria Bioinformatrics Agilent Earray

  • Please log in to reply
2 replies to this topic

#1 Inbox

Inbox

    Veteran

  • Active Members
  • PipPipPipPipPipPipPipPipPipPip
  • 328 posts
21
Excellent

Posted 23 August 2012 - 04:05 AM

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.

#2 toejam

toejam

    Guitar Hero

  • Active Members
  • PipPipPipPipPipPipPipPipPipPip
  • 159 posts
15
Good

Posted 24 September 2012 - 03:37 AM

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.
"When there's no more room in hell the dead will walk the Earth"

#3 Inbox

Inbox

    Veteran

  • Active Members
  • PipPipPipPipPipPipPipPipPipPip
  • 328 posts
21
Excellent

Posted 25 September 2012 - 01:53 AM

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





Home - About - Terms of Service - Privacy - Contact Us

©1999-2013 Protocol Online, All rights reserved.