sequences. An FTP server (ftp://ftp.ncbi.nlm.nih.gov/genomes)
facilitates the bulk download even of larger selections of genomes.2.1.3 Universal Protein
Resource (UniProt) [15]
UniProt has a dedicated database for providing access to the gene
sets (here called “proteomes”) of organisms with a genome
sequence available. Visit the site http://www.uniprot.org/pro-
teomes to access the protein sequences and their annotations.2.1.4 Ensembl [16] Ensembl (http://www.ensembl.org/) is a comprehensive genome
browser for high-quality vertebrate genomes. Ensembl provides
access to the annotated gene sets in the individual genomes via
the data mining tool, BioMart. Ensembl Genomes (http://
ensemblgenomes.org/) extends the genome information of
Ensembl across the taxonomic space and provides access to
non-vertebrate genome resources. Currently, five projects are
maintained dedicated to the genomes of bacteria, plants, protists,
metazoa, and fungi, respectively.
2.1.5 Quest for Orthologs
Reference Proteomes [17]
The Quest For Orthologs (QfO) Reference Proteomes (http://
http://www.ebi.ac.uk/reference_proteomes) is a collection of complete
nonredundant gene sets for a curated compilation of species repre-
senting the three domains of life. Each gene is represented here by
one protein.2.1.6 Others There are several other genome databases that provide access to
potentially relevant sequence data. Among these are the Baylor
College (https://www.hgsc.bcm.edu/), the Saccharomyces
Genome Database (http://www.yeastgenome.org/), the Cryp-
toDB (http://cryptodb.org/cryptodb/), and the Candida
Genome Database (http://www.candidagenome.org/).
2.2 Pathway
Databases
2.2.1 KEGG Pathways
[13]
KEGG pathways (http://www.genome.jp/kegg/pathway.html)
are a collection of manually curated molecular interaction and
reaction networks based on the experimental analysis of well-
studied model organisms.2.2.2 WikiPathways
Database [18]
The WikiPathways database (http://www.wikipathways.org/index.
php/WikiPathways) is an open collaborative project to comple-
ment pathway information available from ongoing efforts, such as
KEGG [13], Reactome [19], or Pathway Commons [20].2.3 Software
for Ortholog Search
2.3.1 InParanoid [21]
InParanoid is a software for identifying orthologs in pairs of species.
According to a recent benchmark [22], the tool provides a good
balance between accuracy and sensitivity. An online database is
available at http://inparanoid.sbc.su.se/cgi-bin/index.cgi, and
the InParanoid software can be downloaded for stand-alone ortho-
log searches.114 Arpit Jain et al.