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The team selected Wisconsin guard-center Peter Konz in the second round.
Holmes, listed at 6-foot-5 and 323 pounds, will have a chance to compete for playing time behind Tyson Clabo and Will Svitek. He played two years at Southern Miss and was a first-team All-Conference USA selection by the league's coaches in 2011.
Holmes transferred to Southern Miss from Itawamba Community College.
The Falcons moved down seven spots in the third round in a trade with Baltimore. Atlanta added the 29th pick of the fifth round, No. 164 overall, in the trade.