looking for plasmid, phage

[mmmm]

how to detect complete plasmid and complete phage/ prophage within contigs (denovo assembled illumina reads) within bacterial genome- annotation will show hundreds of phage proteins or plasmid proteins but is it possible to know the name of the whole plasmid or phage within the assembled bacterial genome/s?

[GenoMax]

Are you expecting to find a specific one or is that a general question about how to identify a plasmid?

[mmmm]

it is a a general question- how to identify the presence of plasmid/ phages within assembled contigs- is there a certain software/ database?- as annotation will reveal the proteins only but not the plasmid/ phage name?

[GenoMax]

I don't see a good database of curated plasmid sequences. You could start by using a set like this: http://www.ncbi.nlm.nih.gov/nuccore/...D+srcdb_refseq[PROP]. You can narrow that list down using a genus level restriction to reduce overall search space. Extra-chromosomal and chromosomal sequences would still pose a challenge.

Only way to know for sure would be to isolate the plasmid(s) from your strain and sequence those.