Finding Taqman Probes For Microbial Contigs.

Question

[Anuraj Nayarisseri]

Hello Guys,

I Performed a Multi - Genome comparison with selected microbial species and got some unique genes. With this i performed clustering. After clustering I got nearly 7 thousand contigs. I used some commercial tools to predict the microarray probes for these contigs. Now i want to find the Taqman Probes for the same contigs. But NCBI probe FTP database does not have abilities to download of all probes for selected organisms groups. Can any one help in this regard.

Thanks in Advance Anuraj

Answer 1

[Pierre Lindenbaum]

The NCBI ESearch utility supports the ORGN field for the probe database. For example to search for the IDs of the murine probes, you would call: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=probe&term=%22Mus%20Musculus%22[ORGN]

Then, (am i wrong ?), it seems that the NCBI EFetch doesn't support the 'probe' database. Doing a little reverse engineering it seems that the FASTA headers in the FTP directory begin with the probe-IDS.

e.g. for 74 (Mus/Musculus)

curl -s "ftp://ftp.ncbi.nih.gov/pub/ProbeDB/antisense.fa.gz" |\
gunzip -c | egrep '^>74[a-z]'
>74b.1:1-19 SiRNA probe for Mus musculus gene Casp9, antisense strand.

[Anuraj Nayarisseri]

My Contigs are from salmonella species. I thought to do a standalone balst against Taqman Probe database of NCBI. but in NCBI only 4 species of salmonella probes are available and also its is very less probes are available.Is there any other way to find the Taqman probes for my contigs.