Using Bioinformatics to Investigate
a CODIS STR Site - in silico PCR

We selected STR D16S539 to study in this example:

• Can we find where this short tandem repeat (STR) is in the human genome?
• Given that it is on chromosome 16 (the "16" in its designation), is the STR in an exon, intron, or intergenic region?


• What 4 base sequence makes up the STR?
• How many repeats are present in the individual whose DNA was the model for chromosome 16?
• How many total bases are there in the DNA fragment that would be amplified in this individual?

The answers to the above questions require an answer to the following question:

What is added to the polymerase chain reaction (PCR) for any STR, that directs amplification of that specific region of the human genome?

[Answer: the specific primers for D16S539]

Performing in silico PCR

• Performing PCR in silico, i.e., searching online files of the National Center for Biotechnical Information (NCBI), analogous to performing PCR in vitro. Just as in vitro PCR relies on the forward primer to direct where to initiate DNA amplification, in silico PCR relies on the forward primer to identify where the STR amplification would begin.The reverse primer (with some manipulation), in silico, identifies where the amplified segment of DNA would terminate. The STR must be between these end points.

We will do this search for you and show you the results on a subsequent page (follow the Promega link below). We will then show you a sequence we cut from the NCBI database and pasted on a page for you to search for the STR.

• Pasting the forward primer (24 bases long) into the European genome database, Ensembl's nBLAST window will allow us to see where this sequence matches a single human site among the 3 billion bases that make up the human genome. [We use Ensembl for this because it gives you a chromosome and genome-wide view that we like.]

How to do the exercise:
First, find the forward primer for D16S539 online. Information about STRs can be found online in the STRbase at www.cstl.nist.gov/biotech/strbase/seq_info.htm. Feel free to explore that page, but to continue the exercise, follow the link we found ...

Linking to the Promega website (Promega manufactures primers for the FBI) we found this page ...

Bioinformatics introduction page