Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CDKAM: a taxonomic classification tool using discriminative k-mers and approximate matching strategies.

ABSTRACT: BACKGROUND:Current taxonomic classification tools use exact string matching algorithms that are effective to tackle the data from the next generation sequencing technology. However, the unique error patterns in the third generation sequencing (TGS) technologies could reduce the accuracy of these programs. RESULTS:We developed a Classification tool using Discriminative K-mers and Approximate Matching algorithm (CDKAM). This approximate matching method was used for searching k-mers, which included two phases, a quick mapping phase and a dynamic programming phase. Simulated datasets as well as real TGS datasets have been tested to compare the performance of CDKAM with existing methods. We showed that CDKAM performed better in many aspects, especially when classifying TGS data with average length 1000-1500 bases. CONCLUSIONS:CDKAM is an effective program with higher accuracy and lower memory requirement for TGS metagenome sequence classification. It produces a high species-level accuracy.

SUBMITTER: Bui VK

PROVIDER: S-EPMC7576720 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

CDKAM: a taxonomic classification tool using discriminative k-mers and approximate matching strategies.

Bui Van-Kien VK Wei Chaochun C

BMC bioinformatics 20201020 1

<h4>Background</h4>Current taxonomic classification tools use exact string matching algorithms that are effective to tackle the data from the next generation sequencing technology. However, the unique error patterns in the third generation sequencing (TGS) technologies could reduce the accuracy of these programs.<h4>Results</h4>We developed a Classification tool using Discriminative K-mers and Approximate Matching algorithm (CDKAM). This approximate matching method was used for searching k-mers, ...[more]

PMID: 33081690

Similar Datasets

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers.

Project description:BackgroundThe problem of supervised DNA sequence classification arises in several fields of computational molecular biology. Although this problem has been extensively studied, it is still computationally challenging due to size of the datasets that modern sequencing technologies can produce.ResultsWe introduce CLARK a novel approach to classify metagenomic reads at the species or genus level with high accuracy and high speed. Extensive experimental results on various metagenomic samples show that the classification accuracy of CLARK is better or comparable to the best state-of-the-art tools and it is significantly faster than any of its competitors. In its fastest single-threaded mode CLARK classifies, with high accuracy, about 32 million metagenomic short reads per minute. CLARK can also classify BAC clones or transcripts to chromosome arms and centromeric regions.ConclusionsCLARK is a versatile, fast and accurate sequence classification method, especially useful for metagenomics and genomics applications. It is freely available at http://clark.cs.ucr.edu/ .

| S-EPMC4428112 | biostudies-literature

CoMeta: classification of metagenomes using k-mers.

Project description:Nowadays, the study of environmental samples has been developing rapidly. Characterization of the environment composition broadens the knowledge about the relationship between species composition and environmental conditions. An important element of extracting the knowledge of the sample composition is to compare the extracted fragments of DNA with sequences derived from known organisms. In the presented paper, we introduce an algorithm called CoMeta (Classification of metagenomes), which assigns a query read (a DNA fragment) into one of the groups previously prepared by the user. Typically, this is one of the taxonomic rank (e.g., phylum, genus), however prepared groups may contain sequences having various functions. In CoMeta, we used the exact method for read classification using short subsequences (k-mers) and fast program for indexing large set of k-mers. In contrast to the most popular methods based on BLAST, where the query is compared with each reference sequence, we begin the classification from the top of the taxonomy tree to reduce the number of comparisons. The presented experimental study confirms that CoMeta outperforms other programs used in this context. CoMeta is available at https://github.com/jkawulok/cometa under a free GNU GPL 2 license.

| S-EPMC4401624 | biostudies-literature

Dynamic partitioning of search patterns for approximate pattern matching using search schemes.

Project description:Search schemes constitute a flexible and generic framework to describe how all approximate occurrences of a search pattern in a text can be found efficiently. We propose an algorithm for the dynamic partitioning of search patterns which can be universally applied to any kind of search scheme and demonstrate that this technique significantly reduces the search space. We present Columba, a software tool written in C++, in which a multitude of search schemes are implemented. We discuss implementation aspects such as memory interleaving of Burrows-Wheeler transform representations and the reduction of redundancy that is inherently associated with the edit distance metric. Ultimately, we demonstrate that Columba has superior performance to the state of the art. Using a single CPU core, Columba is able to retrieve all occurrences of 100,000 Illumina reads and their reverse complements within a maximum edit distance of four in the human genome in less than 3 min.

| S-EPMC8246400 | biostudies-literature

TUIT, a BLAST-based tool for taxonomic classification of nucleotide sequences.

Project description:Pyrosequencing of 16S ribosomal RNA (rRNA) genes has become the gold standard in human microbiome studies. The routine task of taxonomic classification using 16S rRNA reads is commonly performed by the Ribosomal Database Project (RDP) II Classifier, a robust tool that relies on a set of well-characterized reference sequences. However, the RDP II Classifier may be unable to classify a significant part of the data set due to the absence of proper reference sequences. The taxonomic classification for some unclassified sequences might still be performed using BLAST searches against large and frequently updated nucleotide databases. Here we introduce TUIT (Taxonomic Unit Identification Tool)-an efficient open source and platform-independent application that can perform taxonomic classification on its own or can be used in combination with the RDP II Classifier to maximize the taxonomic identification rate. Using a set of simulated DNA sequences, we demonstrate that the algorithm performs taxonomic classification with high specificity for sequences as short as 125 base pairs. TUIT is applicable for 16S rRNA gene sequence classification; however, it is not restricted to 16S rRNA sequences. In addition, TUIT may be used as a complementary tool for effective taxonomic classification of nucleotide sequences generated by many current platforms, such as Roche 454 and Illumina. Stand-alone TUIT is available online at http://sourceforge.net/projects/tuit/.

| S-EPMC4186660 | biostudies-literature

Calibrating models of cancer invasion: parameter estimation using approximate Bayesian computation and gradient matching.

Project description:We present two different methods to estimate parameters within a partial differential equation model of cancer invasion. The model describes the spatio-temporal evolution of three variables-tumour cell density, extracellular matrix density and matrix degrading enzyme concentration-in a one-dimensional tissue domain. The first method is a likelihood-free approach associated with approximate Bayesian computation; the second is a two-stage gradient matching method based on smoothing the data with a generalized additive model (GAM) and matching gradients from the GAM to those from the model. Both methods performed well on simulated data. To increase realism, additionally we tested the gradient matching scheme with simulated measurement error and found that the ability to estimate some model parameters deteriorated rapidly as measurement error increased.

| S-EPMC8206694 | biostudies-literature

Location-Scale Matching for Approximate Quasi-Order Sampling.

Project description:Quasi-orders are reflexive and transitive binary relations and have many applications. Examples are the dependencies of mastery among the problems of a psychological test, or methods such as item tree or Boolean analysis that mine for quasi-orders in empirical data. Data mining techniques are typically tested based on simulation studies with unbiased samples of randomly generated quasi-orders. In this paper, we develop techniques for the approximately representative sampling of quasi-orders. Polynomial regression curves are fitted for the mean and standard deviation of quasi-order size as a function of item number. The resulting regression graphs are seen to be quadratic and linear functions, respectively. The extrapolated values for the mean and standard deviation are used to propose two quasi-order sampling techniques. The discrete method matches these location and scale measures with a transformed discrete distribution directly obtained from the sample. The continuous method uses the normal density function with matched expectation and variance. The quasi-orders are constructed according to the biased randomized doubly inductive construction, however they are resampled to become approximately representative following the matched discrete and continuous distributions. In simulations, we investigate the usefulness of these methods. The location-scale matching approach can cope with very large item sets. Close to representative samples of random quasi-orders are constructed for item numbers up to n = 400.

| S-EPMC6573793 | biostudies-other

Improved algorithms for approximate string matching (extended abstract).

Project description:BackgroundThe problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants of the problem, including comparison of two strings, approximate pattern identification in a string or calculation of the longest common subsequence that two strings share.ResultsWe designed an output sensitive algorithm solving the edit distance problem between two strings of lengths n and m respectively in time O((s - |n - m|).min(m, n, s) + m + n) and linear space, where s is the edit distance between the two strings. This worst-case time bound sets the quadratic factor of the algorithm independent of the longest string length and improves existing theoretical bounds for this problem. The implementation of our algorithm also excels in practice, especially in cases where the two strings compared differ significantly in length.ConclusionWe have provided the design, analysis and implementation of a new algorithm for calculating the edit distance of two strings with both theoretical and practical implications. Source code of our algorithm is available online.

| S-EPMC2648743 | biostudies-literature

SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles.

Project description:BackgroundHomology-based taxonomic assignment is impeded by differences between the unassigned read and reference database, forcing a rank-specific classification to the closest (and possibly incorrect) reference lineage. This assignment may be correct only to a general rank (e.g. order) and incorrect below that rank (e.g. family and genus). Algorithms like LCA avoid this by varying the predicted taxonomic rank based on matches to a set of taxonomic references. LCA and related approaches can be conservative, especially if best matches are taxonomically widespread because of events such as lateral gene transfer (LGT).ResultsOur extension to LCA called SPANNER (similarity profile annotater) uses the set of best homology matches (the LCA Profile) for a given sequence and compares this profile with a set of profiles inferred from taxonomic reference organisms. SPANNER provides an assignment that is less sensitive to LGT and other confounding phenomena. In a series of trials on real and artificial datasets, SPANNER outperformed LCA-style algorithms in terms of taxonomic precision and outperformed best BLAST at certain levels of taxonomic novelty in the dataset. We identify examples where LCA made an overly conservative prediction, but SPANNER produced a more precise and correct prediction.ConclusionsBy using profiles of homology matches to represent patterns of genomic similarity that arise because of vertical and lateral inheritance, SPANNER offers an effective compromise between taxonomic assignment based on best BLAST scores, and the conservative approach of LCA and similar approaches.AvailabilityC++ source code and binaries are freely available at http://kiwi.cs.dal.ca/Software/SPANNER.Contactbeiko@cs.dal.caSupplementary informationSupplementary data are available at Bioinformatics online.

| S-EPMC3712219 | biostudies-literature

Interplay of approximate planning strategies.

Project description:Humans routinely formulate plans in domains so complex that even the most powerful computers are taxed. To do so, they seem to avail themselves of many strategies and heuristics that efficiently simplify, approximate, and hierarchically decompose hard tasks into simpler subtasks. Theoretical and cognitive research has revealed several such strategies; however, little is known about their establishment, interaction, and efficiency. Here, we use model-based behavioral analysis to provide a detailed examination of the performance of human subjects in a moderately deep planning task. We find that subjects exploit the structure of the domain to establish subgoals in a way that achieves a nearly maximal reduction in the cost of computing values of choices, but then combine partial searches with greedy local steps to solve subtasks, and maladaptively prune the decision trees of subtasks in a reflexive manner upon encountering salient losses. Subjects come idiosyncratically to favor particular sequences of actions to achieve subgoals, creating novel complex actions or "options."

| S-EPMC4364207 | biostudies-literature

Taxonomic Classification for Living Organisms Using Convolutional Neural Networks.

Project description:Taxonomic classification has a wide-range of applications such as finding out more about evolutionary history. Compared to the estimated number of organisms that nature harbors, humanity does not have a thorough comprehension of to which specific classes they belong. The classification of living organisms can be done in many machine learning techniques. However, in this study, this is performed using convolutional neural networks. Moreover, a DNA encoding technique is incorporated in the algorithm to increase performance and avoid misclassifications. The algorithm proposed outperformed the state of the art algorithms in terms of accuracy and sensitivity, which illustrates a high potential for using it in many other applications in genome analysis.

| S-EPMC5704239 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data