Since the publication of our article (Roth, Gonnet, and Dessimoz: BMC Bioinformatics 2008 9: 518), we have noticed several errors, which we correct in the following

A Alexeyenko

A Bateman

A Schneider

AC Berglund-Sonnhammer

AK Bjorklund

Alexander CJ Roth

AM Altenhoff

AR Mushegian

C Dessimoz

CEV Storm

Christophe Dessimoz

CM Zmasek

D Fulton

DA Benson

DP Wall

ELL Sonnhammer

Gaston H Gonnet

K Chen

L Jensen

L Li

M Dayhoff

M Farrar

M Gil

M Remm

P Flicek

R Balasubramanian

RA Notebaart

RL Tatusov

RTJMvan der Heijden

TF DeLuca

TF Smith

WM Fitch

English

PubMed

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BMC Bioinformatics
Correction
Algorithm of OMA for large-scale orthology inference
Alexander CJ Roth*, Gaston H Gonnet* and Christophe Dessimoz*
Address: ETH Zurich, and Swiss Institute of Bioinformatics, 8092 Zurich, Switzerland
E-mail: Alexander CJ Roth* - alexande@inf.ethz.ch; Gaston H Gonnet* - gonnet@inf.ethz.ch; Christophe Dessimoz* - cdessimoz@inf.ethz.ch
*Corresponding author
Published: 16 July 2009 Received: 15 July 2009
BMC Bioinformatics 2009, 10:220 doi: 10.1186/1471-2105-10-220 Accepted: 16 July 2009
This article is available from: http://www.biomedcentral.com/1471-2105/10/220
© 2009 Roth et al; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
Since the publication of our article (Roth, Gonnet, and Dessimoz: BMC Bioinformatics 2008 9:
518), we have noticed several errors, which we correct in the following.
Correction
We lately identified inadvertent errors in our publication
[1]. We regret these errors, and offer our sincere
apologizes for the confusion and inconvenience. The
corrections are described in detail in what follows.
Formation of stable pairs
In the main text of section “Formation of stable pairs”,
the formula for stable pair formation is missing a minus
sign after the “greater than” symbol. The sentence should
read:
“Formally, a pair of sequences (x, y) from genomes X
and Y is considered a stable pair if and only if, for all
xi Œ X, xi ≠ x, and for all yj Œ Y, yj ≠ y:
d d k d d
j jxy xy xy xy
− > − −s 2( )
and
d d k d d
i ix y xy x y xy
− > − −s 2( )
where d is a pairwise maximum likelihood distance
estimate and k, the tolerance parameter of the
standard deviation between the two distances,
where s s s2 2 2 2d d d d d dxy xy xy xy xy xyj j j−( ) = ( ) + ( ) − ⋅ ( )ccv , .”
Ortholog clustering
In the subsection “Ortholog clustering”, the example
describing the clustering algorithm suggests that our
algorithm could find best global maximum edge weight
clique partition. This is incorrect, as our current
implementation consists of a k-greedy approximation
algorithm which is not guaranteed to find the best global
maximum edge weight clique. To avoid any confusion,
figure Eight has been updated (Fig. 1 here). The figure
caption remains unchanged, but the numbers reported
in the main text should now read:
“Figure 1A shows a graph with edges between all
vertices except (z1, z2) and (z1, y2), which are
paralogous relations. The highest scoring partition
is {w1, x1, z1}, {y2, z2}, with the total sum of edge
weights of 4·900 = 3600. The score is higher than the
Figure 1
Corrected Figure Eight – Maximum edge weight
cliques for inference of orthologous groups. A An
example graph containing one 4-clique, four 3-cliques, and
eight 2-cliques is provided. The highest edge scoring partition
of the graph is {w1, x1, z1}, {y2, z2}. B A possible evolutionary
scenario corresponding to the graph.
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highest scoring maximum size clique {w1, x1, y2, z2},
{z1}, where the sum of the scores is 2·900 + 4·100 =
2200.”
Figure Ten
In section “Results and discussion”, figure Ten shows the
decrease of the relative number of pairs after each step.
The y-axis in the figure was scaled incorrectly. A corrected
version is provided here (Fig. 2). The caption remains
unchanged.
Bibliography Update
Finally, this correction gives us the opportunity to
update a bibliographic reference: since publication of
our original manuscript, Reference 33 [2], “in press”
then, has been now published. The full reference is
provided below.
References
1. Roth ACJ, Gonnet GH and Dessimoz C: Algorithm of OMA for
large-scale orthology inference. BMC Bioinformatics 2008, 9:518.
2. Altenhoff AM and Dessimoz C: Phylogenetic and Functional
Assessment of Orthologs Inference Projects and Methods.
PLoS Comput Biol 2009, 5:e1000262.
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Figure 2
Corrected Figure Ten – Number of pairs reported
after each step. Each step of the algorithm reduces the
number of pairs, and the largest reduction is observed with
the formation of stable pairs.
BMC Bioinformatics 2009, 10:220 http://www.biomedcentral.com/1471-2105/10/220
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Erratum to: Algorithm of OMA for large-scale orthology inference