NCBI GFF annotation BestRefSeq source

[rkizen]

I couldn't seem to find any information on what the BestRefSeq source is from the NCBI GFF annotation for Gallus Gallus. From what I understand, RefSeq is a pipeline that uses experimental data, Gnomon is a prediction pipeline using homology, and tRNAscan-SE is from the tRNA prediction software.

Is BestRefSeq some sort of high confidence subset of RefSeq?

The file that I am referring to specifically can be found here:
ftp://ftp.ncbi.nlm.nih.gov/genomes/G..._level.gff3.gz

[joelbrockman]

I couldn't seem to find any information on what the BestRefSeq source is from the NCBI GFF annotation for Gallus Gallus. From what I understand, RefSeq is a pipeline that uses experimental data, Gnomon is a prediction pipeline using homology, and tRNAscan-SE is from the tRNA prediction software.

Is BestRefSeq some sort of high confidence subset of RefSeq?

The file that I am referring to specifically can be found here:
ftp://ftp.ncbi.nlm.nih.gov/genomes/G..._level.gff3.gz

I realize this thread is a bit old, but I came across it while searching for "bestrefseq" with similar questions as the original poster. From my reading of The NCBI Eukaryotic Genome Annotation Pipeline ( http://www.ncbi.nlm.nih.gov/genome/a...n_euk/process/ ), it appears that BestRefSeq is short for "Best-placed RefSeq". I think this means that it is the best mapping of the RefSeq sequence to the genome by the annotation pipeline.