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?
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Are you expecting to find a specific one or is that a general question about how to identify a plasmid? -
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?Comment
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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.Comment
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CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).
Despite this, “CRISPR helped turn genome editing from a specialized technique into...07-31-2026, 11:01 AM
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