plasmid annotation

[biocc]

hello, when i assembled a genome, i found a new plasmid. so i tend the function of it. some ORF are obtained with glimer, but it seems there are no significant similar with other proteins in NCBI except one RepB protein. my question is how to annotate orfs in my plasmid.
thaks

[Torst]

hello, when i assembled a genome, i found a new plasmid. so i tend the function of it. some ORF are obtained with glimer, but it seems there are no significant similar with other proteins in NCBI except one RepB protein. my question is how to annotate orfs in my plasmid.
thaks

This is normal. I have annotated many bacterial genomes and plasmids. Most plasmid proteins are still "hypothetical" as no one has studied their function yet.

[artful dodger]

Hello, a question from a newbie. How can I find out if there is a plasmid in my genome in silico if I sequenced it de novo. I've been searching for certain motifs or other plasmid specific sequence features but I don't know whether it is the right thing to do or not. Thank you

[biocc]

Hello, a question from a newbie. How can I find out if there is a plasmid in my genome in silico if I sequenced it de novo. I've been searching for certain motifs or other plasmid specific sequence features but I don't know whether it is the right thing to do or not. Thank you

When I compared contigs assembled de novo with reference sequence, I found several contigs cannot be aligned to it. I picked some long contigs and did reverse PCR. At last, it showed they formed a plasmid.