fasta files from NCBI

[kaps]

Dear all, In creating a local blast database, I downloaded fasta files from ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/ and http://www.ncbi.nlm.nih.gov/sites/nu...=%22Viruses%22[PORG]+AND+srcdb_refseq[PROP]. The former appeared larger than the latter, which of them is better? Do both both contain nr sequences? are they different?

Regards

[maubp]

I would put "virus" or "viral" in the thread title since your question seems to relate directly to viruses.

As I wrote on http://seqanswers.com/forums/showpos...0&postcount=21 using Entrez searches for pulling down sequences can be surprisingly complicated due to inconsistent metadata: http://blastedbio.blogspot.co.uk/201...-chimeras.html

You might be better focusing on a curated virus set like ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/ or ftp://ftp.ncbi.nih.gov/genomes/Viruses/ - see also Brister et al. (2015) NCBI Viral Genomes Resource: http://dx.doi.org/10.1093/nar/gku1207

Which is "better" depends on what you are doing. For reproducibility using an official RefSeq release would be best I think, but this will be a subset of all possible sequences.