The U.S. Department of Justice will investigate the  Chicago  Police Department following protests over the city's handling of last year's killing of a black teenager shot by a white police officer, U.S. Attorney General Loretta Lynch said on Monday.

Lynch's announcement came on the same day that a Cook County prosecutor announced that no charges would be filed in a second 2014 fatal police shooting because the man shot had a gun.

U.S. authorities will look at the department's use of force, including deadly force, among other issues, Lynch said at a news briefing to announce the civil probe.

RELATED: Chicago police account of 2014 shooting differs from video

"Our goal in this investigation ... is not to focus on individuals but to improve systems," Lynch said.

She said federal officials would be investigating "constitutional violations" in one of the nation's largest police departments.

"What we are looking is to see whether or not the police department as a systemic matter has engaged in constitutional violations of policing," the nation's top law enforcement official said.

The announcement comes after almost two weeks of protests in  Chicago  following the release of a 2014 police squad car dashboard video showing police officer Jason Van Dyke emptying his gun into 17-year-old Laquan McDonald, shooting him 16 times. Van Dyke has been charged with first-degree murder.

Mayor Rahm Emanuel, who had initially disagreed with calls for a federal civil rights investigation, said on Monday that he welcomed Lynch's announcement and pledged the city's "complete cooperation."

Emanuel ousted his handpicked police superintendent, Garry McCarthy, last week. He also announced on Sunday that he had replaced the head of the city's Independent Police Review Authority, which reviews police misconduct allegations.

Cook County State's Attorney Anita Alvarez said on Monday that no criminal charges would be filed against  Chicago  Police Officer George Hernandez in the fatal Oct. 12, 2014 police shooting of Ronald Johnson III.

A private attorney for Johnson's family has said that the video showed Johnson did not have a gun.

Alvarez showed police car dashboard video to reporters on Monday, which showed an officer firing at Johnson. She said that Johnson had been asked repeatedly by multiple officers to drop his weapon, and that a 9mm semiautomatic pistol was found with Johnson after he was shot.

“Based upon an objective review of the evidence and the law, we have determined that the prosecution could not establish beyond a reasonable doubt that the actions of Officer Hernandez were not reasonable and permissible under the laws of the state of Illinois,” Alvarez said.

High-profile killings of black men at the hands of mainly white police officers in U.S. cities have prompted a national debate about the use of excessive force by police.

Activists have called for Alvarez's resignation in part because the McDonald investigation took 13 months.

The federal investigation of  Chicago  police follows other high-profile investigations of departments in Ferguson, Missouri and in Cleveland. Baltimore police are also under federal scrutiny.

In Ferguson, a St. Louis suburb which drew national attention following the fatal shooting of an unarmed black teen by a white police officer, federal authorities found racially biased abuses in both the police department and municipal court.

Last December, the Justice Department found that the Cleveland police systematically engaged in excessive use of force.