What are informatics tool to identify a new specific gene for conformation of micro organism?

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Vinaykumar Hallur

Determine which genes you wish to use to develop your PCR by doing a through literature search (use well established/ published primers for your pathogens.) Refer to papers like Rapid detection of food-borne pathogens by using molecular techniques (J Med Microbiol January 2005 vol. 54 no. 1 51-54). After going through the literature you would know which genes have been used and which haven`t. After that make your own list of possible genes which could be used and then go to blast to make primers

Go to http://www.ncbi.nlm.nih.gov/tools/primer-blast/

here you input the nucleotide of interest for which you wish to develop primers and then just click on get primers

You will get a list of primers, Narrow down the list for your primers by looking for characters of an ideal primer set like: length of primers sets , complementarity , desired melting temperature, whether any secondary structures are formed or not .

After this, use these sets and input these sequences in box for forward and reverse primer in http://www.ncbi.nlm.nih.gov/tools/primer-blast/, choose nr in the boxes to look into the nucleotide database to look for similarity.

You will get the list of all nucleotides from all organisms which could be amplified by your primers..

This will tell you whether the primer designed by you is specific to your organism or not

MAYTHAM ABBAS ALZUHAIRI

Dear siva Mallika Donepudi ,

What do you mean? Are you looking for new gene finding?

Anyway, if you want specific identification you have to look for 16sRNA for prokaryotic and 18SRNA for eukaryotic regarding identification of microorganism but if you look for new genes the problem will be different.

Thanks