Abstract:
BACKGROUND:Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions. If primary and secondary contigs are not properly identified, the primary assembly will overrepresent both the size and complexity of the genome, which complicates downstream analysis such as scaffolding. RESULTS:Here we illustrate a new method, which we call HapSolo, that identifies secondary contigs and defines a primary assembly based on multiple pairwise contig alignment metrics. HapSolo evaluates candidate primary assemblies using BUSCO scores and then distinguishes among candidate assemblies using a cost function. The cost function can be defined by the user but by default considers the number of missing, duplicated and single BUSCO genes within the assembly. HapSolo performs hill climbing to minimize cost over thousands of candidate assemblies. We illustrate the performance of HapSolo on genome data from three species: the Chardonnay grape (Vitis vinifera), with a genome of 490 Mb, a mosquito (Anopheles funestus; 200 Mb) and the Thorny Skate (Amblyraja radiata; 2650 Mb). CONCLUSIONS:HapSolo rapidly identified candidate assemblies that yield improvements in assembly metrics, including decreased genome size and improved N50 scores. Contig N50 scores improved by 35%, 9% and 9% for Chardonnay, mosquito and the thorny skate, respectively, relative to unreduced primary assemblies. The benefits of HapSolo were amplified by down-stream analyses, which we illustrated by scaffolding with Hi-C data. We found, for example, that prior to the application of HapSolo, only 52% of the Chardonnay genome was captured in the largest 19 scaffolds, corresponding to the number of chromosomes. After the application of HapSolo, this value increased to ~ 84%. The improvements for the mosquito's largest three scaffolds, representing the number of chromosomes, were from 61 to 86%, and the improvement was even more pronounced for thorny skate. We compared the scaffolding results to assemblies that were based on PurgeDups for identifying secondary contigs, with generally superior results for HapSolo.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Solares EA,Tao Y,Long AD,Gaut BSdoi
10.1186/s12859-020-03939-ysubject
Has Abstractpub_date
2021-01-06 00:00:00pages
9issue
1issn
1471-2105pii
10.1186/s12859-020-03939-yjournal_volume
22pub_type
杂志文章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:Cancer progression is caused by the sequential accumulation of mutations, but not all orders of accumulation are equally likely. When the fixation of some mutations depends on the presence of previous ones, identifying restrictions in the order of accumulation of mutations can lead to the discovery of therap...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0466-7
更新日期:2015-02-12 00:00:00
abstract:BACKGROUND:Alternative splicing is the critical process in a single gene coding, which removes introns and joins exons, and splicing branchpoints are indicators for the alternative splicing. Wet experiments have identified a great number of human splicing branchpoints, but many branchpoints are still unknown. In order ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1875-6
更新日期:2017-12-01 00:00:00
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
更新日期:2020-03-12 00:00:00
abstract:BACKGROUND:Data are the evidentiary basis for scientific hypotheses, analyses and publication, for policy formation and for decision-making. They are essential to the evaluation and testing of results by peer scientists both present and future. There is broad consensus in the scientific and conservation communities tha...
journal_title:BMC bioinformatics
pub_type: 指南,杂志文章
doi:10.1186/1471-2105-12-S15-S1
更新日期:2011-01-01 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: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: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
abstract:BACKGROUND:Last generations of Single Nucleotide Polymorphism (SNP) arrays allow to study copy-number variations in addition to genotyping measures. RESULTS:MPAgenomics, standing for multi-patient analysis (MPA) of genomic markers, is an R-package devoted to: (i) efficient segmentation and (ii) selection of genomic ma...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-014-0394-y
更新日期:2014-12-14 00:00:00
abstract:BACKGROUND:Parsimony and maximum likelihood methods of phylogenetic tree estimation and parsimony methods for genome rearrangements are central to the study of genome evolution yet to date they have largely been pursued in isolation. RESULTS:We present a data structure called a history graph that offers a practical ba...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-206
更新日期:2014-06-19 00:00:00
abstract:BACKGROUND:As high-throughput sequencing applications continue to evolve, the rapid growth in quantity and variety of sequence-based data calls for the development of new software libraries and tools for data analysis and visualization. Often, effective use of these tools requires computational skills beyond those of m...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03577-4
更新日期:2020-06-29 00:00:00
abstract:BACKGROUND:MLPA method is a potentially useful semi-quantitative method to detect copy number alterations in targeted regions. In this paper, we propose a method for the normalization procedure based on a non-linear mixed-model, as well as a new approach for determining the statistical significance of altered probes ba...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-261
更新日期:2008-06-04 00:00:00
abstract:BACKGROUND:The complexity and dynamics of microbial communities are major factors in the ecology of a system. With the NGS technique, metagenomics data provides a new way to explore microbial interactions. Lotka-Volterra models, which have been widely used to infer animal interactions in dynamic systems, have recently ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1359-0
更新日期:2016-11-25 00:00:00
abstract:BACKGROUND:Low diversity of the gut microbiome, often progressing to the point of intestinal domination by a single species, has been linked to poor outcomes in patients undergoing hematopoietic cell transplantation (HCT). Our ability to understand how certain organisms attain intestinal domination over others has been...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3073-1
更新日期:2019-12-02 00:00:00
abstract::Following publication of the original article [1], the author reported that there are several errors in the original article. ...
journal_title:BMC bioinformatics
pub_type: 杂志文章,已发布勘误
doi:10.1186/s12859-019-3318-z
更新日期:2020-01-22 00:00:00
abstract:BACKGROUND:Testing the dependence of two variables is one of the fundamental tasks in statistics. In this work, we developed an open-source R package (knnAUC) for detecting nonlinear dependence between one continuous variable X and one binary dependent variables Y (0 or 1). RESULTS:We addressed this problem by using k...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2427-4
更新日期:2018-11-22 00:00:00
abstract:BACKGROUND:Recent studies have shown that N6-methyladenosine (m6A) plays a critical role in numbers of biological processes and complex human diseases. However, the regulatory mechanisms of most methylation sites remain uncharted. Thus, in-depth study of the epi-transcriptomic patterns of m6A may provide insights into ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03787-w
更新日期:2020-10-09 00:00:00
abstract:BACKGROUND:High-throughput experiments, such as with DNA microarrays, typically result in hundreds of genes potentially relevant to the process under study, rendering the interpretation of these experiments problematic. Here, we propose and evaluate an approach to find functional associations between large numbers of g...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-14
更新日期:2007-01-18 00:00:00
abstract:BACKGROUND:Supercomputers have become indispensable infrastructures in science and industries. In particular, most state-of-the-art scientific results utilize massively parallel supercomputers ranked in TOP500. However, their use is still limited in the bioinformatics field due to the fundamental fact that the asynchro...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3085-x
更新日期:2019-12-02 00:00:00
abstract:BACKGROUND:Bistability and ability to switch between two stable states is the hallmark of cellular responses. Cellular signaling pathways often contain bistable switches that regulate the transmission of the extracellular information to the nucleus where important biological functions are executed. RESULTS:In this wor...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3155-0
更新日期:2019-11-28 00:00:00
abstract:BACKGROUND:There are a number of different methods for generation of trees and algorithms for phylogenetic analysis in the study of bacterial taxonomy. Genotypic information, such as SSU rRNA gene sequences, now plays a more prominent role in microbial systematics than does phenotypic information. However, the integrat...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-281
更新日期:2007-08-02 00:00:00
abstract:BACKGROUND:The topology of a biological pathway provides clues as to how a pathway operates, but rationally using this topology information with observed gene expression data remains a challenge. RESULTS:We introduce a new general-purpose analytic method called Mechanistic Bayesian Networks (MBNs) that allows for the ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-433
更新日期:2009-12-18 00:00:00
abstract:BACKGROUND:The main goal of the whole transcriptome analysis is to correctly identify all expressed transcripts within a specific cell/tissue--at a particular stage and condition--to determine their structures and to measure their abundances. RNA-seq data promise to allow identification and quantification of transcript...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-135
更新日期:2014-05-09 00:00:00
abstract:BACKGROUND:Manual chemical data curation from publications is error-prone, time consuming, and hard to maintain up-to-date data sets. Automatic information extraction can be used as a tool to reduce these problems. Since chemical structures usually described in images, information extraction needs to combine structure ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-S17-S9
更新日期:2012-01-01 00:00:00
abstract:BACKGROUND:Protein remote homology detection and fold recognition are central problems in bioinformatics. Currently, discriminative methods based on support vector machine (SVM) are the most effective and accurate methods for solving these problems. A key step to improve the performance of the SVM-based methods is to f...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-510
更新日期:2008-12-01 00:00:00
abstract:BACKGROUND:Intracellular signal transduction is achieved by networks of proteins and small molecules that transmit information from the cell surface to the nucleus, where they ultimately effect transcriptional changes. Understanding the mechanisms cells use to accomplish this important process requires a detailed molec...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-3-34
更新日期:2002-11-01 00:00:00
abstract:BACKGROUND:Recent advances in genomics and proteomics have allowed us to study the nuances of the Warburg effect--a long-standing puzzle in cancer energy metabolism--at an unprecedented level of detail. While modern next-generation sequencing technologies are extremely powerful, the lack of appropriate data analysis to...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-S10-S8
更新日期:2011-10-18 00:00:00
abstract:BACKGROUND:Accurate annotation of translation initiation sites (TISs) is essential for understanding the translation initiation mechanism. However, the reliability of TIS annotation in widely used databases such as RefSeq is uncertain due to the lack of experimental benchmarks. RESULTS:Based on a homogeneity assumptio...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-160
更新日期:2008-03-25 00:00:00
abstract:BACKGROUND:In many bacteria, intragenomic diversity in synonymous codon usage among genes has been reported. However, no quantitative attempt has been made to compare the diversity levels among different genomes. Here, we introduce a mean dissimilarity-based index (Dmean) for quantifying the level of diversity in synon...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-167
更新日期:2009-06-01 00:00:00
abstract:BACKGROUND:The Bioinformatics Resource Manager (BRM) is a web-based tool developed to facilitate identifier conversion and data integration for Homo sapiens (human), Mus musculus (mouse), Rattus norvegicus (rat), Danio rerio (zebrafish), and Macaca mulatta (macaque), as well as perform orthologous conversions among the...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-2805-6
更新日期:2019-05-17 00:00:00