Abstract:
BACKGROUND:Quadruplexes are specific structure motifs occurring, e.g., in telomeres and transcriptional regulatory regions. Recent discoveries confirmed their importance in biomedicine and led to an intensified examination of their properties. So far, the study of these motifs has focused mainly on the sequence and the tertiary structure, and concerned canonical structures only. Whereas, more and more non-canonical quadruplex motifs are being discovered. RESULTS:Here, we present ElTetrado, a software that identifies quadruplexes (composed of guanine- and other nucleobase-containing tetrads) in nucleic acid structures and classifies them according to the recently introduced ONZ taxonomy. The categorization is based on the secondary structure topology of quadruplexes and their component tetrads. It supports the analysis of canonical and non-canonical motifs. Besides the class recognition, ElTetrado prepares a dot-bracket and graphical representations of the secondary structure, which reflect the specificity of the quadruplex's structure topology. It is implemented as a freely available, standalone application, available at https://github.com/tzok/eltetrado. CONCLUSIONS:The proposed software tool allows to identify and classify tetrads and quadruplexes based on the topology of their secondary structures. It complements existing approaches focusing on the sequence and 3D structure.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Zok T,Popenda M,Szachniuk Mdoi
10.1186/s12859-020-3385-1subject
Has Abstractpub_date
2020-01-31 00:00:00pages
40issue
1issn
1471-2105pii
10.1186/s12859-020-3385-1journal_volume
21pub_type
杂志文章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
更新日期:2008-01-27 00:00:00
abstract:BACKGROUND:Molecular biology (MB) is a dynamic research domain that benefits greatly from the use of modern software technology in preparing experiments, analyzing acquired data, and even performing "in-silico" analyses. As ever new findings change the face of this domain, software for MB has to be sufficiently flexibl...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-97
更新日期:2009-03-27 00:00:00
abstract:BACKGROUND:Most single stranded RNA (ssRNA) viruses mutate rapidly to generate large number of strains having highly divergent capsid sequences. Accurate strain recognition in uncharacterized target capsid sequences is essential for epidemiology, diagnostics, and vaccine development. Strain recognition based on similar...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-379
更新日期:2007-10-10 00:00:00
abstract:BACKGROUND:Transcription factors are known to play key roles in carcinogenesis and therefore, are gaining popularity as potential therapeutic targets in drug development. A 'master regulator' transcription factor often appears to control most of the regulatory activities of the other transcription factors and the assoc...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1499-x
更新日期:2017-02-02 00:00:00
abstract:BACKGROUND:Protein structure comparison is a fundamental task in structural biology. While the number of known protein structures has grown rapidly over the last decade, searching a large database of protein structures is still relatively slow using existing methods. There is a need for new techniques which can rapidly...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-S1-S46
更新日期:2010-01-18 00:00:00
abstract:BACKGROUND:Formal classification of a large collection of protein structures aids the understanding of evolutionary relationships among them. Classifications involving manual steps, such as SCOP and CATH, face the challenge of increasing volume of available structures. Automatic methods such as FSSP or Dali Domain Dict...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-74
更新日期:2008-01-31 00:00:00
abstract:BACKGROUND:The specific recognition of genomic cis-regulatory elements by transcription factors (TFs) plays an essential role in the regulation of coordinated gene expression. Studying the mechanisms determining binding specificity in protein-DNA interactions is thus an important goal. Most current approaches for model...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-436
更新日期:2008-10-16 00:00:00
abstract:BACKGROUND:Microorganisms display vast diversity, and each one has its own set of genes, cell components and metabolic reactions. To assess their huge unexploited metabolic potential in different ecosystems, we need high throughput tools, such as functional microarrays, that allow the simultaneous analysis of thousands...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-478
更新日期:2010-09-23 00:00:00
abstract:BACKGROUND:The central element of each enzyme is the catalytic site, which commonly catalyzes a single biochemical reaction with high specificity. It was unclear to us how often sites that catalyze the same or highly similar reactions evolved on different, i. e. non-homologous protein folds and how similar their 3D pos...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0807-6
更新日期:2015-11-04 00:00:00
abstract:BACKGROUND:An organism's protein interactome, or complete network of protein-protein interactions, defines the protein complexes that drive cellular processes. Techniques for studying protein complexes have traditionally applied targeted strategies such as yeast two-hybrid or affinity purification-mass spectrometry to ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1865-8
更新日期:2017-10-23 00:00:00
abstract:BACKGROUND:Detection of periodically expressed genes from microarray data without use of known periodic and non-periodic training examples is an important problem, e.g. for identifying genes regulated by the cell-cycle in poorly characterised organisms. Commonly the investigator is only interested in genes expressed at...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-63
更新日期:2006-02-09 00:00:00
abstract:BACKGROUND:Periodic phenomena are widespread in biology. The problem of finding periodicity in biological time series can be viewed as a multiple hypothesis testing of the spectral content of a given time series. The exact noise characteristics are unknown in many bioinformatics applications. Furthermore, the observed ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-117
更新日期:2005-05-13 00:00:00
abstract:BACKGROUND:The challenge of classifying cortical interneurons is yet to be solved. Data-driven classification into established morphological types may provide insight and practical value. RESULTS:We trained models using 217 high-quality morphologies of rat somatosensory neocortex interneurons reconstructed by a single...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2470-1
更新日期:2018-12-17 00:00:00
abstract:BACKGROUND:Protein-protein interactions (PPIs) are central to many biological processes. Considering that the experimental methods for identifying PPIs are time-consuming and expensive, it is important to develop automated computational methods to better predict PPIs. Various machine learning methods have been proposed...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03646-8
更新日期:2020-07-21 00:00:00
abstract:BACKGROUND:The developments of high-throughput genotyping technologies, which enable the simultaneous genotyping of hundreds of thousands of single nucleotide polymorphisms (SNP) have the potential to increase the benefits of genetic epidemiology studies. Although the enhanced resolution of these platforms increases th...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-102
更新日期:2009-04-03 00:00:00
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
更新日期:2009-06-16 00:00:00
abstract:BACKGROUND:Mass spectrometry is an essential analytical technique for high-throughput analysis in proteomics and metabolomics. The development of new separation techniques, precise mass analyzers and experimental protocols is a very active field of research. This leads to more complex experimental setups yielding ever ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-163
更新日期:2008-03-26 00:00:00
abstract:BACKGROUND:Protein structure prediction has achieved a lot of progress during the last few decades and a greater number of models for a certain sequence can be predicted. Consequently, assessing the qualities of predicted protein models in perspective is one of the key components of successful protein structure predict...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1691-z
更新日期:2017-05-25 00:00:00
abstract:BACKGROUND:G-DOC Plus is a data integration and bioinformatics platform that uses cloud computing and other advanced computational tools to handle a variety of biomedical BIG DATA including gene expression arrays, NGS and medical images so that they can be analyzed in the full context of other omics and clinical inform...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1010-0
更新日期:2016-04-30 00:00:00
abstract:BACKGROUND:Carbohydrates are a class of large and diverse biomolecules, ranging from a simple monosaccharide to large multi-branching glycan structures. The covalent linkage of a carbohydrate to the nitrogen atom of an asparagine, a process referred to as N-linked glycosylation, plays an important role in the physiolog...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3097-6
更新日期:2019-10-22 00:00:00
abstract:BACKGROUND:Set comparisons permeate a large number of data analysis workflows, in particular workflows in biological sciences. Venn diagrams are frequently employed for such analysis but current tools are limited. RESULTS:We have developed InteractiVenn, a more flexible tool for interacting with Venn diagrams includin...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0611-3
更新日期:2015-05-22 00:00:00
abstract:BACKGROUND:Mechanistic models are becoming more and more popular in Systems Biology; identification and control of models underlying biochemical pathways of interest in oncology is a primary goal in this field. Unfortunately the scarce availability of data still limits our understanding of the intrinsic characteristics...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-S12-S4
更新日期:2009-10-15 00:00:00
abstract:BACKGROUND:The identification of genes responsible for human inherited diseases is one of the most challenging tasks in human genetics. Recent studies based on phenotype similarity and gene proximity have demonstrated great success in prioritizing candidate genes for human diseases. However, most of these methods rely ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-S1-S11
更新日期:2011-02-15 00:00:00
abstract:BACKGROUND:Interest in de novo genome assembly has been renewed in the past decade due to rapid advances in high-throughput sequencing (HTS) technologies which generate relatively short reads resulting in highly fragmented assemblies consisting of contigs. Additional long-range linkage information is typically used to ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-S9-S9
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Cross-species comparisons of gene neighborhoods (also called genomic contexts) in microbes may provide insight into determining functionally related or co-regulated sets of genes, suggest annotations of previously un-annotated genes, and help to identify horizontal gene transfer events across microbial speci...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-18
更新日期:2013-01-16 00:00:00
abstract:BACKGROUND:Blood pressure diseases have increasingly been identified as among the main factors threatening human health. How to accurately and conveniently measure blood pressure is the key to the implementation of effective prevention and control measures for blood pressure diseases. Traditional blood pressure measure...
journal_title:BMC bioinformatics
pub_type: 临床试验,杂志文章
doi:10.1186/s12859-019-2667-y
更新日期:2019-02-28 00:00:00
abstract:BACKGROUND:Here we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-0887-y
更新日期:2016-01-20 00:00:00
abstract:BACKGROUND:Clustering of unannotated transcripts is an important task to identify novel families of noncoding RNAs (ncRNAs). Several hierarchical clustering methods have been developed using similarity measures based on the scores of structural alignment. However, the high computational cost of exact structural alignme...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-S1-S48
更新日期:2011-02-15 00:00:00
abstract:BACKGROUND:Protein solvent accessibility prediction is a pivotal intermediate step towards modeling protein tertiary structures directly from one-dimensional sequences. It also plays an important part in identifying protein folds and domains. Although some methods have been presented to the protein solvent accessibilit...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0851-2
更新日期:2016-01-11 00:00:00
abstract:BACKGROUND:Alternative splicing is a major contributor to the diversity of eukaryotic transcriptomes and proteomes. Currently, large scale detection of alternative splicing using expressed sequence tags (ESTs) or microarrays does not capture all alternative splicing events. Moreover, for many species genomic data is be...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-477
更新日期:2008-11-12 00:00:00