Exercise 5

Use targetRNA to predict bacterial mRNA targets for GcvB RNA.

• Are there any conserved targets between E. coli and Y. pestis?
• Use RNAup, IntaRNA, RNAcofold and RNAhybrid to investigate a putative interaction between E. coli dppA and GcvB RNA.

>E.coli.1 GcvB

ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGGUGAACUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGA

UUCAGACCAUGGUAGCAAAGCUACCUUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCUAAUUGCGGUGCUUUUUUUU

>Y.pestis.1 GcvB

ACUUCCCCUAGCCGGAACGAAAAGUAGGUUUGGUAUCCCAGGUACUGAAAUGCUUUUGGCUUUGUGGUGGUGAUGUUGUGUUUGCAAAUGGUCUGGUAUGCCA

GACAUAGUAGCUAAGCUACUGCUUUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUUUAUGCAGCACCGUUAUUUUGGCGGUGCUUUUUUUU

>E.coli_dppA

GCAAAGGGUUAAAACAACAAACAUCACAAUUGGAGCAGAAUAAUGCGUAUUUCCUUGAAAAAGUCAGGGAUGCUGAAGCUUGGUCUCAGCCUGGUGGCUAU