databases in ncbi
Hi, I was wondering what the difference was between the ncbi nucleotide nt/nr database was to the refseq genome database and the refseq representative genome database?
When I search for alignments to my assembly in these databases, I get a very low query cover using the latter two databases, and very good query cover using nt/Nr... Is this just because it's a bigger database? Could there be anything wrong with my assembly?
Thank you
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guardsquirrel •
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RefSeq is a manually curated subset of the genbank/nr/nt databases for high quality reference sequences (hence the name). There will be significantly more matches in the other databases to your query. There's nothing to suggest that would be indicative of something being wrong with your data, but also doesn't rule it out, so it depends on the specific alignments etc you're getting back...