The Securities and Exchange Commission has reportedly set its sights on the often-mysterious world of high-frequency trading, questioning whether these sophisticated traders' cozy relationship with exchanges gives them an unfair advantage.

According to The Wall Street Journal, the SEC probe is zeroing in on the computer-driven trading platforms of exchanges, including BATS Global Markets, which ironically is debuting as a public company on Friday just as the news breaks.

High-frequency trading firms, which tend to avoid the limelight, have come into focus in the wake of the May 2010 “flash crash,” which featured a brief 1,000-point plunge on the Dow after glitches in computer-trading systems. These traders use advanced and powerful computer systems to rapidly execute trades, often ahead of most other investors.

SEC investigators are probing whether high-frequency trading firms “collude” to limit competition or manipulate markets, the paper reported, adding that regulators have requested more information from a number of high-speed firms and their communications with exchanges.

The SEC is investigating the trading activities of Chicago-based Getco and Tradebot Systems, each of which have invested in BATS, the Journal reported.

At the same time, the SEC is probing communications between rapid-fire firms and Jersey City, N.J.-based Direct Edge Holdings, the paper said.

The report comes at an awful time for BATS, which priced its IPO at the low end of expectations Thursday night and is poised to begin trading on Friday.

While not nearly as well known as its larger peers, the Lenexa, Kan.-based company accounts for about 11% of average daily volume, trailing only exchanges operated by NYSE Euronext (NYX) and Nasdaq OMX Group (NDAQ).

BATS is the first IPO by a U.S. exchange since options market operator CBOE (CBOE) debuted in 2010.

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