Insertion and deletion correcting DNA barcodes based on watermarks.

Abstract:

BACKGROUND:Barcode multiplexing is a key strategy for sharing the rising capacity of next-generation sequencing devices: Synthetic DNA tags, called barcodes, are attached to natural DNA fragments within the library preparation procedure. Different libraries, can individually be labeled with barcodes for a joint sequencing procedure. A post-processing step is needed to sort the sequencing data according to their origin, utilizing these DNA labels. The final separation step is called demultiplexing and is mainly determined by the characteristics of the DNA code words used as labels. Currently, we are facing two different strategies for barcoding: One is based on the Hamming distance, the other uses the edit metric to measure distances of code words. The theory of channel coding provides well-known code constructions for Hamming metric. They provide a large number of code words with variable lengths and maximal correction capability regarding substitution errors. However, some sequencing platforms are known to have exceptional high numbers of insertion or deletion errors. Barcodes based on the edit distance can take insertion and deletion errors into account in the decoding process. Unfortunately, there is no explicit code-construction known that gives optimal codes for edit metric. RESULTS:In the present work we focus on an entirely different perspective to obtain DNA barcodes. We consider a concatenated code construction, producing so-called watermark codes, which were first proposed by Davey and Mackay, to communicate via binary channels with synchronization errors. We adapt and extend the concepts of watermark codes to use them for DNA sequencing. Moreover, we provide an exemplary set of barcodes that are experimentally compatible with common next-generation sequencing platforms. Finally, a realistic simulation scenario is use to evaluate the proposed codes to show that the watermark concept is suitable for DNA sequencing applications. CONCLUSION:Our adaption of watermark codes enables the construction of barcodes that are capable of correcting substitutions, insertion and deletion errors. The presented approach has the advantage of not needing any markers or technical sequences to recover the position of the barcode in the sequencing reads, which poses a significant restriction with other approaches.

journal_name

BMC Bioinformatics

journal_title

BMC bioinformatics

authors

Kracht D,Schober S

doi

10.1186/s12859-015-0482-7

subject

Has Abstract

pub_date

2015-02-18 00:00:00

pages

50

issn

1471-2105

pii

10.1186/s12859-015-0482-7

journal_volume

16

pub_type

杂志文章
  • Estimation of evolutionary parameters using short, random and partial sequences from mixed samples of anonymous individuals.

    abstract:BACKGROUND:Over the last decade, next generation sequencing (NGS) has become widely available, and is now the sequencing technology of choice for most researchers. Nonetheless, NGS presents a challenge for the evolutionary biologists who wish to estimate evolutionary genetic parameters from a mixed sample of unlabelled...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-015-0810-y

    authors: Wu SH,Rodrigo AG

    更新日期:2015-11-04 00:00:00

  • Comparative evaluation of gene-set analysis methods.

    abstract:BACKGROUND:Multiple data-analytic methods have been proposed for evaluating gene-expression levels in specific biological pathways, assessing differential expression associated with a binary phenotype. Following Goeman and Bühlmann's recent review, we compared statistical performance of three methods, namely Global Tes...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-8-431

    authors: Liu Q,Dinu I,Adewale AJ,Potter JD,Yasui Y

    更新日期:2007-11-07 00:00:00

  • Statistical assessment and visualization of synergies for large-scale sparse drug combination datasets.

    abstract:BACKGROUND:Drug combinations have the potential to improve efficacy while limiting toxicity. To robustly identify synergistic combinations, high-throughput screens using full dose-response surface are desirable but require an impractical number of data points. Screening of a sparse number of doses per drug allows to sc...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-019-2642-7

    authors: Amzallag A,Ramaswamy S,Benes CH

    更新日期:2019-02-18 00:00:00

  • Colonyzer: automated quantification of micro-organism growth characteristics on solid agar.

    abstract:BACKGROUND:High-throughput screens comparing growth rates of arrays of distinct micro-organism cultures on solid agar are useful, rapid methods of quantifying genetic interactions. Growth rate is an informative phenotype which can be estimated by measuring cell densities at one or more times after inoculation. Precise ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-11-287

    authors: Lawless C,Wilkinson DJ,Young A,Addinall SG,Lydall DA

    更新日期:2010-05-28 00:00:00

  • Cyclic nucleotide binding proteins in the Arabidopsis thaliana and Oryza sativa genomes.

    abstract:BACKGROUND:Cyclic nucleotides are ubiquitous intracellular messengers. Until recently, the roles of cyclic nucleotides in plant cells have proven difficult to uncover. With an understanding of the protein domains which can bind cyclic nucleotides (CNB and GAF domains) we scanned the completed genomes of the higher plan...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-6-6

    authors: Bridges D,Fraser ME,Moorhead GB

    更新日期:2005-01-11 00:00:00

  • The scoring of poses in protein-protein docking: current capabilities and future directions.

    abstract:BACKGROUND:Protein-protein docking, which aims to predict the structure of a protein-protein complex from its unbound components, remains an unresolved challenge in structural bioinformatics. An important step is the ranking of docked poses using a scoring function, for which many methods have been developed. There is ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-14-286

    authors: Moal IH,Torchala M,Bates PA,Fernández-Recio J

    更新日期:2013-10-01 00:00:00

  • Bacterial protein meta-interactomes predict cross-species interactions and protein function.

    abstract:BACKGROUND:Protein-protein interactions (PPIs) can offer compelling evidence for protein function, especially when viewed in the context of proteome-wide interactomes. Bacteria have been popular subjects of interactome studies: more than six different bacterial species have been the subjects of comprehensive interactom...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-017-1585-0

    authors: Caufield JH,Wimble C,Shary S,Wuchty S,Uetz P

    更新日期:2017-03-16 00:00:00

  • Network hub-node prioritization of gene regulation with intra-network association.

    abstract:BACKGROUND:To identify and prioritize the influential hub genes in a gene-set or biological pathway, most analyses rely on calculation of marginal effects or tests of statistical significance. These procedures may be inappropriate since hub nodes are common connection points and therefore may interact with other nodes ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-020-3444-7

    authors: Chang HC,Chu CP,Lin SJ,Hsiao CK

    更新日期:2020-03-12 00:00:00

  • Efficient prediction of human protein-protein interactions at a global scale.

    abstract:BACKGROUND:Our knowledge of global protein-protein interaction (PPI) networks in complex organisms such as humans is hindered by technical limitations of current methods. RESULTS:On the basis of short co-occurring polypeptide regions, we developed a tool called MP-PIPE capable of predicting a global human PPI network ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-014-0383-1

    authors: Schoenrock A,Samanfar B,Pitre S,Hooshyar M,Jin K,Phillips CA,Wang H,Phanse S,Omidi K,Gui Y,Alamgir M,Wong A,Barrenäs F,Babu M,Benson M,Langston MA,Green JR,Dehne F,Golshani A

    更新日期:2014-12-10 00:00:00

  • Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments.

    abstract:BACKGROUND:High-throughput sequencing technologies, such as the Illumina Genome Analyzer, are powerful new tools for investigating a wide range of biological and medical questions. Statistical and computational methods are key for drawing meaningful and accurate conclusions from the massive and complex datasets generat...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-11-94

    authors: Bullard JH,Purdom E,Hansen KD,Dudoit S

    更新日期:2010-02-18 00:00:00

  • MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data.

    abstract:BACKGROUND:Mass spectrometry (MS) coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well as proteomic research. Such approaches are used for systems biology, functional genomics, and biomarker discovery, among others. An ongoin...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-11-395

    authors: Pluskal T,Castillo S,Villar-Briones A,Oresic M

    更新日期:2010-07-23 00:00:00

  • Vertical decomposition with Genetic Algorithm for Multiple Sequence Alignment.

    abstract:BACKGROUND:Many Bioinformatics studies begin with a multiple sequence alignment as the foundation for their research. This is because multiple sequence alignment can be a useful technique for studying molecular evolution and analyzing sequence structure relationships. RESULTS:In this paper, we have proposed a Vertical...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-12-353

    authors: Naznin F,Sarker R,Essam D

    更新日期:2011-08-25 00:00:00

  • FocAn: automated 3D analysis of DNA repair foci in image stacks acquired by confocal fluorescence microscopy.

    abstract:BACKGROUND:Phosphorylated histone H2AX, also known as γH2AX, forms μm-sized nuclear foci at the sites of DNA double-strand breaks (DSBs) induced by ionizing radiation and other agents. Due to their specificity and sensitivity, γH2AX immunoassays have become the gold standard for studying DSB induction and repair. One o...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-020-3370-8

    authors: Memmel S,Sisario D,Zimmermann H,Sauer M,Sukhorukov VL,Djuzenova CS,Flentje M

    更新日期:2020-01-28 00:00:00

  • Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour 'rules'.

    abstract:BACKGROUND:Metabolomics experiments using Mass Spectrometry (MS) technology measure the mass to charge ratio (m/z) and intensity of ionised molecules in crude extracts of complex biological samples to generate high dimensional metabolite 'fingerprint' or metabolite 'profile' data. High resolution MS instruments perform...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-10-227

    authors: Draper J,Enot DP,Parker D,Beckmann M,Snowdon S,Lin W,Zubair H

    更新日期:2009-07-21 00:00:00

  • Nonparametric relevance-shifted multiple testing procedures for the analysis of high-dimensional multivariate data with small sample sizes.

    abstract:BACKGROUND:In many research areas it is necessary to find differences between treatment groups with several variables. For example, studies of microarray data seek to find a significant difference in location parameters from zero or one for ratios thereof for each variable. However, in some studies a significant deviat...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-9-54

    authors: Frömke C,Hothorn LA,Kropf S

    更新日期:2008-01-27 00:00:00

  • A computational approach for detecting peptidases and their specific inhibitors at the genome level.

    abstract:BACKGROUND:Peptidases are proteolytic enzymes responsible for fundamental cellular activities in all organisms. Apparently about 2-5% of the genes encode for peptidases, irrespectively of the organism source. The basic peptidase function is "protein digestion" and this can be potentially dangerous in living organisms w...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-8-S1-S3

    authors: Bartoli L,Calabrese R,Fariselli P,Mita DG,Casadio R

    更新日期:2007-03-08 00:00:00

  • In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation.

    abstract:BACKGROUND:Microarray co-expression signatures are an important tool for studying gene function and relations between genes. In addition to genuine biological co-expression, correlated signals can result from technical deficiencies like hybridization of reporters with off-target transcripts. An approach that is able to...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-8-461

    authors: Casneuf T,Van de Peer Y,Huber W

    更新日期:2007-11-26 00:00:00

  • Structural alignment of protein descriptors - a combinatorial model.

    abstract:BACKGROUND:Structural alignment of proteins is one of the most challenging problems in molecular biology. The tertiary structure of a protein strictly correlates with its function and computationally predicted structures are nowadays a main premise for understanding the latter. However, computationally derived 3D model...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-016-1237-9

    authors: Antczak M,Kasprzak M,Lukasiak P,Blazewicz J

    更新日期:2016-09-17 00:00:00

  • Identification and utilization of inter-species conserved (ISC) probesets on Affymetrix human GeneChip platforms for the optimization of the assessment of expression patterns in non human primate (NHP) samples.

    abstract:BACKGROUND:While researchers have utilized versions of the Affymetrix human GeneChip for the assessment of expression patterns in non human primate (NHP) samples, there has been no comprehensive sequence analysis study undertaken to demonstrate that the probe sequences designed to detect human transcripts are reliably ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-5-165

    authors: Wang Z,Lewis MG,Nau ME,Arnold A,Vahey MT

    更新日期:2004-10-26 00:00:00

  • OpWise: operons aid the identification of differentially expressed genes in bacterial microarray experiments.

    abstract:BACKGROUND:Differentially expressed genes are typically identified by analyzing the variation between replicate measurements. These procedures implicitly assume that there are no systematic errors in the data even though several sources of systematic error are known. RESULTS:OpWise estimates the amount of systematic e...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-7-19

    authors: Price MN,Arkin AP,Alm EJ

    更新日期:2006-01-13 00:00:00

  • Preliminary nanopore cheminformatics analysis of aptamer-target binding strength.

    abstract:BACKGROUND:Aptamers are nucleic acids selected for their ability to bind to molecules of interest and may provide the basis for a whole new class of medicines. If the aptamer is simply a dsDNA molecule with a ssDNA overhang (a "sticky" end) then the segment of ssDNA that complements that overhang provides a known bindi...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-8-S7-S11

    authors: Thomson K,Amin I,Morales E,Winters-Hilt S

    更新日期:2007-11-01 00:00:00

  • Reranking candidate gene models with cross-species comparison for improved gene prediction.

    abstract:BACKGROUND:Most gene finders score candidate gene models with state-based methods, typically HMMs, by combining local properties (coding potential, splice donor and acceptor patterns, etc). Competing models with similar state-based scores may be distinguishable with additional information. In particular, functional and...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-9-433

    authors: Liu Q,Crammer K,Pereira FC,Roos DS

    更新日期:2008-10-14 00:00:00

  • SDAR: a practical tool for graphical analysis of two-dimensional data.

    abstract:BACKGROUND:Two-dimensional data needs to be processed and analysed in almost any experimental laboratory. Some tasks in this context may be performed with generic software such as spreadsheet programs which are available ubiquitously, others may require more specialised software that requires paid licences. Additionall...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-13-201

    authors: Weeratunga S,Hu NJ,Simon A,Hofmann A

    更新日期:2012-08-14 00:00:00

  • An evaluation of copy number variation detection tools for cancer using whole exome sequencing data.

    abstract:BACKGROUND:Recently copy number variation (CNV) has gained considerable interest as a type of genomic/genetic variation that plays an important role in disease susceptibility. Advances in sequencing technology have created an opportunity for detecting CNVs more accurately. Recently whole exome sequencing (WES) has beco...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-017-1705-x

    authors: Zare F,Dow M,Monteleone N,Hosny A,Nabavi S

    更新日期:2017-05-31 00:00:00

  • Sample entropy analysis of cervical neoplasia gene-expression signatures.

    abstract:BACKGROUND:We introduce Approximate Entropy as a mathematical method of analysis for microarray data. Approximate entropy is applied here as a method to classify the complex gene expression patterns resultant of a clinical sample set. Since Entropy is a measure of disorder in a system, we believe that by choosing genes...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-10-66

    authors: Botting SK,Trzeciakowski JP,Benoit MF,Salama SA,Diaz-Arrastia CR

    更新日期:2009-02-20 00:00:00

  • Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model.

    abstract:BACKGROUND:Large-scale genomic studies often identify large gene lists, for example, the genes sharing the same expression patterns. The interpretation of these gene lists is generally achieved by extracting concepts overrepresented in the gene lists. This analysis often depends on manual annotation of genes based on c...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-11-272

    authors: He X,Sarma MS,Ling X,Chee B,Zhai C,Schatz B

    更新日期:2010-05-20 00:00:00

  • The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays.

    abstract:BACKGROUND:Gene expression studies greatly contribute to our understanding of complex relationships in gene regulatory networks. However, the complexity of array design, production and manipulations are limiting factors, affecting data quality. The use of customized DNA microarrays improves overall data quality in many...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-11-112

    authors: Vainshtein Y,Sanchez M,Brazma A,Hentze MW,Dandekar T,Muckenthaler MU

    更新日期:2010-03-01 00:00:00

  • Towards barcode markers in Fungi: an intron map of Ascomycota mitochondria.

    abstract:BACKGROUND:A standardized and cost-effective molecular identification system is now an urgent need for Fungi owing to their wide involvement in human life quality. In particular the potential use of mitochondrial DNA species markers has been taken in account. Unfortunately, a serious difficulty in the PCR and bioinform...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-10-S6-S15

    authors: Santamaria M,Vicario S,Pappadà G,Scioscia G,Scazzocchio C,Saccone C

    更新日期:2009-06-16 00:00:00

  • GenHtr: a tool for comparative assessment of genetic heterogeneity in microbial genomes generated by massive short-read sequencing.

    abstract:BACKGROUND:Microevolution is the study of short-term changes of alleles within a population and their effects on the phenotype of organisms. The result of the below-species-level evolution is heterogeneity, where populations consist of subpopulations with a large number of structural variations. Heterogeneity analysis ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-11-508

    authors: Yu G

    更新日期:2010-10-12 00:00:00

  • PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.

    abstract:BACKGROUND:The number of protein structures from structural genomics centers dramatically increases in the Protein Data Bank (PDB). Many of these structures are functionally unannotated because they have no sequence similarity to proteins of known function. However, it is possible to successfully infer function using o...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-7-53

    authors: von Grotthuss M,Plewczynski D,Ginalski K,Rychlewski L,Shakhnovich EI

    更新日期:2006-02-06 00:00:00