Genome Download from NCBI

Question

[akhilesh.mishra88]

Hello,

I want to download RefSeq entry of genomes for my research, I want to know what do I use in RefSeq Category option of Assembly Database, Did I use "Reference Genome" or "Representative Genome" and what is the difference between them.

[PoGibas]

See sections "Reference Genome" and "Representative Genome".

Answer 1

[Rafael Puche]

Hello akhilesh.mishra88 this a differences:

Reference genome

Manually selected 'gold standard' complete genomes with high-quality annotation and the highest level of experimental support for structural and functional annotation. They include community-curated genomes if the annotation quality meets 'reference genome' requirements that are manually reviewed by NCBI staff http://www.ncbi.nlm.nih.gov/genome/browse/reference/

Representative genome

Representative genome for an organism (species); for some diverse species can be more than one. Corresponds to Sequence Ontology-[SO:0001505] (9). www.ncbi.nlm.nih.gov/genome/browse/representative/

Nucleic Acids Research, 2014, Vol. 42, Database issue D553-D559

Answer 2

[Juke34]

By the way, I heard from some researchers that sometimes the NCBI annotation is worse than the original annotation submitted to GeneBank. In refseq you will find only annotation done by NCBI.