All the projects included in this study are publicly available. A short
description of the chosen configurations and references are given in the
following. We used the default parameters unless mentioned otherwise.
RoundUp: RoundUp can be downloaded from https://rodeo.med.harvard.edu/tools/roundup/ . It is available
with different parameter settings to tune for the desired sensitivity. In this
comparison we included the strictest parameter set (also default settings), i.e.
Blast E-value cutoff 10−20 and divergence cutoff 0.2.
Inparanoid: Inparanoid is available from http://inparanoid.sbc.su.se . We used the release 6.0 from Aug
2007 including 35 species.
Ensembl Compara: The orthology predictions from Ensembl were
obtained from the Compara database version 47, which is available fromhttp://oct2007.archive.ensembl.org/ .
COG,KOG: Cluster of Orthologous Groups and its eukaryotic equivalent
are available fromhttp://www.ncbi.nlm.nih.gov/COG/ . We used the versions from Mar
2003 and Jul 2003 respectively.
OrthoMCL: We obtained the version from Sep 2006 of OrthoMCL from
http://orthomcl.cbil.upenn.edu/ .
Homologene: Homologene is available from the NCBI webpage www.ncbi.nlm.nih.gov/HomoloGene/ . For this comparison, we used
built 58 from Nov 2007.
EggNOG: EggNOG is available from http://eggnog.embl.de/ . We
used the data from Oct 2007 including 373 species.
OMA: OMA is available in various formats on http://www.omabrowser.org . We used the the data from Nov 2007
including 550 species. OMA infer orthology at the level of pairs of sequences
(“OMA Pairwise”), from which it also computes groups of
orthologs (“OMA Group”). Both type of predictions are
included in the comparisons.
BBH: The typical Bidirectional Best Hit implementation uses BLAST
for aligning the protein sequences. We used the more accurate algorithm from
Smith and Waterman [35] (link) for the alignment with the same scoring
threshold as used by the OMA algorithm for the all-against-all step.
RSD: Reciprocal Smallest Distance orthology relations are computed
using ML distance estimates from pairwise alignments having significant
alignment scores (Dayhoff score >217, the cut-off used by OMA as
well)
description of the chosen configurations and references are given in the
following. We used the default parameters unless mentioned otherwise.
with different parameter settings to tune for the desired sensitivity. In this
comparison we included the strictest parameter set (also default settings), i.e.
Blast E-value cutoff 10−20 and divergence cutoff 0.2.
2007 including 35 species.
obtained from the Compara database version 47, which is available from
are available from
2003 and Jul 2003 respectively.
built 58 from Nov 2007.
used the data from Oct 2007 including 373 species.
including 550 species. OMA infer orthology at the level of pairs of sequences
(“OMA Pairwise”), from which it also computes groups of
orthologs (“OMA Group”). Both type of predictions are
included in the comparisons.
for aligning the protein sequences. We used the more accurate algorithm from
Smith and Waterman [35] (link) for the alignment with the same scoring
threshold as used by the OMA algorithm for the all-against-all step.
using ML distance estimates from pairwise alignments having significant
alignment scores (Dayhoff score >217, the cut-off used by OMA as
well)
Free full text: Click here
