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.
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fasta files from NCBI
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?
RegardsLast edited by kaps; 02-02-2015, 04:46 AM.
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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