Open Access

Erratum to: MetCap: A bioinformatics probe design pipeline for large-scale targeted metagenomics

  • Sandeep K. Kushwaha1Email author,
  • Lokeshwaran Manoharan1,
  • Tejashwari Meerupati1,
  • Katarina Hedlund1 and
  • Dag Ahren1, 2
BMC BioinformaticsBMC series – open, inclusive and trusted201617:39

https://doi.org/10.1186/s12859-015-0843-2

Received: 10 December 2015

Accepted: 11 December 2015

Published: 18 January 2016

The original article was published in BMC Bioinformatics 2015 16:65

Erratum

In our article [1], the numbers of probes and sequences for the CAZy dataset in the Additional file 3, table S3 (A) (Table 1 here) have been switched. The corrected table S3 (A) is presented in this erratum.
Table 1

(A): Family-wise summary of generated probes based on sequences downloaded from CAZy database

Family

Archaea

Bacteria

Eukaryota

Unclassified

Virus

Total probes

Total sequences

CBM

439

26910

7424

134

453

35360

23302

CE

311

14646

3254

66

9

18286

13787

GH

2754

97488

33643

1457

7382

142724

110923

GT

7755

106687

30802

160

683

146087

103952

PL

57

4663

1082

6

51

5859

6580

Total

11316

250394

76205

1823

8578

348316

258544

In the following three parts of our article [1] we would like to correct the numbers for probes and sequences accordingly.

Abstract (Results), page 1

To illustrate the advantage of a targeted metagenome approach, we have generated more than 400,000 probes that match more than 300,000 publicly available sequences related to carbon degradation, and used these probes for targeted sequencing in a soil metagenome study.

Results and discussion, page 6

In this study, 306,525 nucleotide sequences were extracted through the pipeline and used as a proof of concept. A list of group-wise collected sequences and generated probes from databases are given as Additional file 3: Table S3. In total, 406,277 unique probes were produced from these extracted nucleotide sequences in this study with the following criteria: length (50mer), GC contents (35-65), melting temperature (55-65), and 3 probes per cluster on 90 % cluster similarity.

Results and discussion, page 8

Among the downloaded sequences (Additional file 3: Table S3), 258,544 sequences belong to the CAZy database from four major families: Glycoside Hydrolase (110,923), Glycosyl Transferases (103,952), Carbohydrate Esterases (13,787), Polysaccharide Lyases (6,580), and an associated module, Carbohydrate binding-modules (23,302) and 348,316 probes have been designed from these sequences.

Notes

Declarations

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Authors’ Affiliations

(1)
Department of Biology, Lund University
(2)
Bioinformatics Infrastructure for Life Sciences (BILS), Department of Biology, Lund University

Reference

  1. Kushwaha SK, Manoharan L, Meerupati T, Hedlund K, Ahren D. MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics. BMC Bioinformatics. 2015;16:65.PubMedPubMed CentralView ArticleGoogle Scholar

Copyright

© Kushwaha et al. 2016

Advertisement