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. 2015 Sep 22;10(9):e0139006. doi: 10.1371/journal.pone.0139006

Table 1. Sources of protein sequence data used in this study.

Sources of protein sequence data URL Ref.
National Centre for Biotechnology Information (NCBI) ftp://ftp.ncbi.nlm.nih.gov/genomes [10]
European Bioinformatics Institute- European Nucleotide Archive (EBI-ENA) ftp://ftp.ebi.ac.uk/pub/software/ensembl/eg-dumps/blast-11 [22]
ENSEMBL ftp://ftp.ensembl.org/pub/release-65/fasta [12]
Broad Institute Database http://www.broadinstitute.org/scientific-community/data
Department of Energy Joint Genome Institute (DOE-JGI) ftp://ftp.jgi-psf.org/pub/JGI_data
J. Craig Venter Institute (JCVI) ftp://ftp.jcvi.org/pub/data/Eukaryotic_Project
Beijing Genomics Institute (BGI) ftp://ftp.genomics.org.cn/pub [14]
Consensus CDS Project (CCDS) http://www.ncbi.nlm.nih.gov/CCDS [23]
Génolevures http://www.genolevures.org [24]
Genoscope http://www.genoscope.cns.fr/spip/Genoscope-s-Resources.html
Saccharomyces Genome Database (SGD) http://www.yeastgenome.org [11]
Wormbase https://www.wormbase.org [16]
Flybase https://flybase.org [13]
The Arabidopsis Information Resource (TAIR) https://www.arabidopsis.org [18]
Rice Genome Annotation Project http://rice.plantbiology.msu.edu [21]
Genome Database for Rosaceae (GDR) http://www.rosaceae.org [17]
VectorBase https://www.vectorbase.org/downloads [15]
Bioinformatics & Evolutionary Genomics Lab at Ghent University http://bioinformatics.psb.ugent.be/genomes/
SUPERFAMILY http://supfam2.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/index.html [20]
Cyanidioschyzon merolae Genome Project http://merolae.biol.s.u-tokyo.ac.jp/download/ [19]