(Reuters) - A federal judge has thrown out much of Prudential Financial Inc's (>> Prudential Financial Inc) lawsuit accusing Bank of America Corp (>> Bank of America Corp) of defrauding it before the financial crisis into buying more than $1.9 billion (1 billion pounds) of residential mortgage-backed securities that later soured.

In a decision on Thursday, U.S. District Judge Stanley Chesler in Newark, New Jersey, said Prudential did not show that Bank of America and its Merrill Lynch unit lied to rating agencies about the quality of loans backing its securities.

He also said Prudential could not rely on "after-the-fact" computer analysis to show the defendants knew when arranging the 54 securitisation at issue from 2004 to 2007 that property appraisals were being systematically inflated.

Chesler, who previously dismissed Prudential's racketeering claim, threw out most of the Newark-based insurer's remaining claims with prejudice.

He said Prudential may resubmit one claim involving 21 securitisation where the defendants acted as underwriters, not sponsors or issuers. The judge did not rule on Prudential's "equitable fraud" claim.

Prudential spokesman Scot Hoffman and Bank of America spokesman Lawrence Grayson declined to comment.

The lawsuit said Bank of America's "wide-ranging fraud" left Prudential stuck with securities backed by "countless" home loans that went into default or foreclosure, or lacked proper title.

Prudential said 51.8 percent of the 20,906 home loans it examined had at least one material defect.

Bank of America, the second-largest U.S. bank, in August reached a $16.65 billion (11 billion pound) settlement with federal and state authorities to resolve many of its mortgage-related liabilities linked to the recent U.S. housing and financial crises.

The Charlotte, North Carolina-based bank plans to appeal a $1.27 billion civil penalty imposed in a U.S. government lawsuit accusing its Countrywide unit of defrauding government-controlled mortgage companies Fannie Mae (>> Federal National Mortgage Assctn Fnni Me) and Freddie Mac (>> Federal Home Loan Mortgage Corp) into buying questionable home loans.

U.S. District Judge Jed Rakoff in Manhattan set that penalty last July, and on Tuesday rejected Bank of America's request to overturn it.

The case is Prudential Insurance Co of America et al v. Bank of America NA et al, U.S. District Court, District of New Jersey, No. 13-01586.

(Reporting by Jonathan Stempel in New York; Editing by Lisa Von Ahn)

By Jonathan Stempel