Comparison of annotated genomes

Question

[marina-orlova]

Hello

I need to compare a de-novo assembled scaffold to reference genome (proteins etc.). We have prokka output for pathogenic strain of e.coli (gbk with annotation, gff, faa with proteins etc.). Are there any tools capable to compare proteins list in gbk or faa files?

[HG]

You can have a look to get some idea

http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0006291&representation=PDF

[Juke34]

Have a look here (Figure 1 explains well what the tool does)

This may help you.