Abstract:
BACKGROUND:Genetic variations predispose individuals to hereditary diseases, play important role in the development of complex diseases, and impact drug metabolism. The full information about the DNA variations in the genome of an individual is given by haplotypes, the ordered lists of single nucleotide polymorphisms (SNPs) located on chromosomes. Affordable high-throughput DNA sequencing technologies enable routine acquisition of data needed for the assembly of single individual haplotypes. However, state-of-the-art high-throughput sequencing platforms generate data that is erroneous, which induces uncertainty in the SNP and genotype calling procedures and, ultimately, adversely affect the accuracy of haplotyping. When inferring haplotype phase information, the vast majority of the existing techniques for haplotype assembly assume that the genotype information is correct. This motivates the development of methods capable of joint genotype calling and haplotype assembly. RESULTS:We present a haplotype assembly algorithm, ParticleHap, that relies on a probabilistic description of the sequencing data to jointly infer genotypes and assemble the most likely haplotypes. Our method employs a deterministic sequential Monte Carlo algorithm that associates single nucleotide polymorphisms with haplotypes by exhaustively exploring all possible extensions of the partial haplotypes. The algorithm relies on genotype likelihoods rather than on often erroneously called genotypes, thus ensuring a more accurate assembly of the haplotypes. Results on both the 1000 Genomes Project experimental data as well as simulation studies demonstrate that the proposed approach enables highly accurate solutions to the haplotype assembly problem while being computationally efficient and scalable, generally outperforming existing methods in terms of both accuracy and speed. CONCLUSIONS:The developed probabilistic framework and sequential Monte Carlo algorithm enable joint haplotype assembly and genotyping in a computationally efficient manner. Our results demonstrate fast and highly accurate haplotype assembly aided by the re-examination of erroneously called genotypes. A C code implementation of ParticleHap will be available for download from https://sites.google.com/site/asynoeun/particlehap.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Ahn S,Vikalo Hdoi
10.1186/s12859-015-0651-8subject
Has Abstractpub_date
2015-07-16 00:00:00pages
223issn
1471-2105pii
10.1186/s12859-015-0651-8journal_volume
16pub_type
杂志文章abstract:BACKGROUND:Abruptness of pigment patterns at the periphery of a skin lesion is one of the most important dermoscopic features for detection of malignancy. In current clinical setting, abrupt cutoff of a skin lesion determined by an examination of a dermatologist. This process is subjective, nonquantitative, and error-p...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1892-5
更新日期:2017-12-28 00:00:00
abstract:BACKGROUND:Recent studies in computational primary protein sequence analysis have leveraged the power of unlabeled data. For example, predictive models based on string kernels trained on sequences known to belong to particular folds or superfamilies, the so-called labeled data set, can attain significantly improved acc...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-S4-S2
更新日期:2009-04-29 00:00:00
abstract:BACKGROUND:In metabolomics experiments, spectral fingerprints of metabolites with no known structural identity are detected routinely. Computer-assisted structure elucidation (CASE) has been used to determine the structural identities of unknown compounds. It is generally accepted that a single 1D NMR spectrum or mass ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-234
更新日期:2014-07-05 00:00:00
abstract:BACKGROUND:Reverse engineering of transcriptional regulatory networks (TRN) from genomics data has always represented a computational challenge in System Biology. The major issue is modeling the complex crosstalk among transcription factors (TFs) and their target genes, with a method able to handle both the high number...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-3510-1
更新日期:2020-05-29 00:00:00
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
更新日期:2007-11-01 00:00:00
abstract:BACKGROUND:Physical maps have been historically one of the cornerstones of genome sequencing and map-based cloning strategies. They also support marker assisted breeding and EST mapping. The problem of building a high quality physical map is computationally challenging due to unavoidable noise in the input fingerprint ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-217
更新日期:2009-07-15 00:00:00
abstract:BACKGROUND:Next Generation Sequencing (NGS) is a commonly used technology for studying the genetic basis of biological processes and it underpins the aspirations of precision medicine. However, there are significant challenges when dealing with NGS data. Firstly, a huge number of bioinformatics tools for a wide range o...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-2791-8
更新日期:2019-04-27 00:00:00
abstract:BACKGROUND:The Damerau-Levenshtein (DL) distance metric has been widely used in the biological science. It tries to identify the similar region of DNA,RNA and protein sequences by transforming one sequence to the another using the substitution, insertion, deletion and transposition operations. Lowrance and Wagner have ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3184-8
更新日期:2020-12-09 00:00:00
abstract:BACKGROUND:Somatic copy number alternation (SCNA) is a common feature of the cancer genome and is associated with cancer etiology and prognosis. The allele-specific SCNA analysis of a tumor sample aims to identify the allele-specific copy numbers of both alleles, adjusting for the ploidy and the tumor purity. Next gene...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2412-y
更新日期:2018-11-14 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:UNLABELLED: BACKGROUND:Acquiring and exploring whole genome sequence information for a species under investigation is now a routine experimental approach. On most genome browsers, typically, only the DNA sequence, EST support, motif search results, and GO annotations are displayed. However, for many species, a growing...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-447
更新日期:2011-11-15 00:00:00
abstract:BACKGROUND:Antibacterial peptides are important components of the innate immune system, used by the host to protect itself from different types of pathogenic bacteria. Over the last few decades, the search for new drugs and drug targets has prompted an interest in these antibacterial peptides. We analyzed 486 antibacte...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-263
更新日期:2007-07-23 00:00:00
abstract:BACKGROUND:Microarray technology has become very popular for globally evaluating gene expression in biological samples. However, non-linear variation associated with the technology can make data interpretation unreliable. Therefore, methods to correct this kind of technical variation are critical. Here we consider a me...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-520
更新日期:2008-12-04 00:00:00
abstract:BACKGROUND:Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings i...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-421
更新日期:2009-12-15 00:00:00
abstract:BACKGROUND:Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic seq...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-227
更新日期:2014-06-30 00:00:00
abstract:BACKGROUND:The wide use of high-throughput DNA microarray technology provide an increasingly detailed view of human transcriptome from hundreds to thousands of genes. Although biomedical researchers typically design microarray experiments to explore specific biological contexts, the relationships between genes are hard...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-S5-S7
更新日期:2011-01-01 00:00:00
abstract:BACKGROUND:The Acel_2062 protein from Acidothermus cellulolyticus is a protein of unknown function. Initial sequence analysis predicted that it was a metallopeptidase from the presence of a motif conserved amongst the Asp-zincins, which are peptidases that contain a single, catalytic zinc ion ligated by the histidines ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-1
更新日期:2014-01-03 00:00:00
abstract:BACKGROUND:The knowledge base-driven pathway analysis is becoming the first choice for many investigators, in that it not only can reduce the complexity of functional analysis by grouping thousands of genes into just several hundred pathways, but also can increase the explanatory power for the experiment by identifying...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1285-1
更新日期:2016-10-06 00:00:00
abstract:BACKGROUND:Computer simulation is a resource which can be employed to identify optimal breeding strategies to effectively and efficiently achieve specific goals in developing improved cultivars. In some instances, it is crucial to assess in silico the options as well as the impact of various crossing schemes and breedi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-0906-z
更新日期:2016-02-06 00:00:00
abstract:BACKGROUND:As part of its broad and ambitious mission, the MicroArray Quality Control (MAQC) project reported the results of experiments using External RNA Controls (ERCs) on five microarray platforms. For most platforms, several different methods of data processing were considered. However, there was no similar consid...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-371
更新日期:2007-10-03 00:00:00
abstract:BACKGROUND:Identifying the interactions between proteins and long non-coding RNAs (lncRNAs) is of great importance to decipher the functional mechanisms of lncRNAs. However, current experimental techniques for detection of lncRNA-protein interactions are limited and inefficient. Many methods have been proposed to predi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2390-0
更新日期:2018-10-11 00:00:00
abstract:BACKGROUND:In binary high-throughput screening projects where the goal is the identification of low-frequency events, beyond the obvious issue of efficiency, false positives and false negatives are a major concern. Pooling constitutes a natural solution: it reduces the number of tests, while providing critical duplicat...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-28
更新日期:2006-01-19 00:00:00
abstract:BACKGROUND:Reliability and Reproducibility of differentially expressed genes (DEGs) are essential for the biological interpretation of microarray data. The microarray quality control (MAQC) project launched by US Food and Drug Administration (FDA) elucidated that the lists of DEGs generated by intra- and inter-platform...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-143
更新日期:2013-04-29 00:00:00
abstract:BACKGROUND:Patient records contain valuable information regarding explanation of diagnosis, progression of disease, prescription and/or effectiveness of treatment, and more. Automatic recognition of clinically important concepts and the identification of relationships between those concepts in patient records are preli...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-S3-S3
更新日期:2011-06-09 00:00:00
abstract:BACKGROUND:Eisenia fetida, commonly known as red wiggler or compost worm, belongs to the Lumbricidae family of the Annelida phylum. Little is known about its genome sequence although it has been extensively used as a test organism in terrestrial ecotoxicology. In order to understand its gene expression response to envi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-S7-S7
更新日期:2007-11-01 00:00:00
abstract:BACKGROUND:Sequence motifs representing transcription factor binding sites (TFBS) are commonly encoded as position frequency matrices (PFM) or degenerate consensus sequences (CS). These formats are used to represent the characterised TFBS profiles stored in transcription factor databases, as well as to represent the po...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-189
更新日期:2007-06-08 00:00:00
abstract:BACKGROUND:With the growing availability of full-text articles online, scientists and other consumers of the life sciences literature now have the ability to go beyond searching bibliographic records (title, abstract, metadata) to directly access full-text content. Motivated by this emerging trend, I posed the followin...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-46
更新日期:2009-02-03 00:00:00
abstract:BACKGROUND:Fluorescent reporter genes have become widely used for monitoring gene expression in living cells. When a microbial strain carrying a reporter gene is grown in a microplate reader, the fluorescence and the absorbance (optical density) of the culture can be automatically measured every few minutes in a highly...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-2920-4
更新日期:2019-06-11 00:00:00
abstract:BACKGROUND:Enrichment analysis is a popular approach to identify pathways or sets of genes which are significantly enriched in the context of differentially expressed genes. The traditional gene set enrichment approach considers a pathway as a simple gene list disregarding any knowledge of gene or protein interactions....
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0751-5
更新日期:2015-10-22 00:00:00
abstract:BACKGROUND:Feed-forward loops (FFLs), consisting of miRNAs, transcription factors (TFs) and their common target genes, have been validated to be important for the initialization and development of complex diseases, including cancer. Esophageal Carcinoma (ESCA) and Stomach Adenocarcinoma (STAD) are two types of malignan...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3230-6
更新日期:2019-12-30 00:00:00