Literature DB >> 27933096

Erratum to: A representation of a compressed de Bruijn graph for pan-genome analysis that enables search.

Abstract

[This corrects the article DOI: 10.1186/s13015-016-0083-7.].

Entities: Species

Year: 2016 PMID： 27933096 PMCID： PMC5126863 DOI： 10.1186/s13015-016-0090-8

Source DB: PubMed Journal: Algorithms Mol Biol ISSN： 1748-7188 Impact factor: 1.405

Erratum to: Algorithms Mol Biol (2016) 11:20 DOI 10.1186/s13015-016-0083-7

After publication of the original article [1], the authors noticed errors in Algorithm 2 and the caption of Table 4. In Algorithm 2, the term “rank1(Bl, i − 1) + 1” should be included on line 28 and not line 29. In addition, in the caption of Table 4, the word “BVr” should be replaced by “Br” and the word “BVl” should be replaced by “Bl”. The correct versions of Algorithm 2 and Table 4 are included in this erratum.

Table 4

Breakdown of the space usage of the variants of Algorithm A4

Algorithm	Part	62 E.coli	7 × Chr1	7 × HG
A4	wt-bwt	0.42 (23.83%)	0.44 (36.23%)	0.43 (22.68%)
A4	Nodes	0.10 (5.94%)	0.03 (2.61%)	0.04 (2.02%)
A4	\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$B_r$$\end{document}Br	0.16 (8.93%)	0.16 (12.86%)	0.16 (8.25%)
A4	\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$B_l$$\end{document}Bl	0.14 (8.04%)	0.14 (11.57%)	0.14 (7.42%)
A4	wt-doc	0.93 (53.26%)	0.45 (36.73%)	1.13 (59.63%)
A4compr1	wt-bwt	0.42 (28.57%)	0.44 (47.83%)	0.43 (26.85%)
A4compr1	Nodes	0.10 (7.12%)	0.03 (3.44%)	0.04 (2.39%)
A4compr1	\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$B_r$$\end{document}Br	0.00 (0.23%)	0.00 (0.12%)	0.00 (0.09%)
A4compr1	\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$B_l$$\end{document}Bl	0.00 (0.23%)	0.00 (0.12%)	0.00 (0.08%)
A4compr1	wt-doc	0.93 (63.85%)	0.45 (48.49%)	1.13 (70.59%)
A4compr2	wt-bwt	0.16 (13.03%)	0.22 (31.01%)	0.22 (15.62%)
A4compr2	Nodes	0.10 (8.67%)	0.03 (4.55%)	0.04 (2.76%)
A4compr2	\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$B_r$$\end{document}Br	0.00 (0.28%)	0.00 (0.16%)	0.00 (0.10%)
A4compr2	\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$B_l$$\end{document}Bl	0.00 (0.28%)	0.00 (0.16%)	0.00 (0.10%)
A4compr2	wt-doc	0.93 (77.74%)	0.45 (64.11%)	1.13 (81.42%)

The first column shows the algorithm used in the experiment (the k-mer size is 50). The second column specifies the different data structures used: wt-bwt stands for the wavelet tree of the (including rank and select support), nodes stands for the array of nodes (the implicit graph representation), and are the bit vectors described in “Computation of right-maximal k-mers and node identifiers” section (including rank support), and wt-doc stands for the wavelet tree of the document array. The remaining columns show the memory usage in bytes per base pair and, in parentheses, their percentage

Breakdown of the space usage of the variants of Algorithm A4 The first column shows the algorithm used in the experiment (the k-mer size is 50). The second column specifies the different data structures used: wt-bwt stands for the wavelet tree of the (including rank and select support), nodes stands for the array of nodes (the implicit graph representation), and are the bit vectors described in “Computation of right-maximal k-mers and node identifiers” section (including rank support), and wt-doc stands for the wavelet tree of the document array. The remaining columns show the memory usage in bytes per base pair and, in parentheses, their percentage

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1. A representation of a compressed de Bruijn graph for pan-genome analysis that enables search.

Authors: Timo Beller; Enno Ohlebusch
Journal: Algorithms Mol Biol Date: 2016-07-18 Impact factor: 1.405

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