Abstract:
BACKGROUND:Coalescent simulations have proven very useful in many population genetics studies. In order to arrive to meaningful conclusions, it is important that these simulations resemble the process of molecular evolution as much as possible. To date, no single coalescent program is able to simulate codon sequences sampled from populations with recombination, migration and growth. RESULTS:We introduce a new coalescent program, called Recodon, which is able to simulate samples of coding DNA sequences under complex scenarios in which several evolutionary forces can interact simultaneously (namely, recombination, migration and demography). The basic codon model implemented is an extension to the general time-reversible model of nucleotide substitution with a proportion of invariable sites and among-site rate variation. In addition, the program implements non-reversible processes and mixtures of different codon models. CONCLUSION:Recodon is a flexible tool for the simulation of coding DNA sequences under realistic evolutionary models. These simulations can be used to build parameter distributions for testing evolutionary hypotheses using experimental data. Recodon is written in C, can run in parallel, and is freely available from http://darwin.uvigo.es/.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Arenas M,Posada Ddoi
10.1186/1471-2105-8-458subject
Has Abstractpub_date
2007-11-20 00:00:00pages
458issn
1471-2105pii
1471-2105-8-458journal_volume
8pub_type
杂志文章abstract:BACKGROUND:A rapidly increasing flow of genomic data requires the development of efficient methods for obtaining its compact representation. Feature extraction facilitates classification, clustering and model analysis for testing and refining biological hypotheses. "Shotgun" metagenome is an analytically challenging ty...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0875-7
更新日期:2016-01-16 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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abstract:BACKGROUND:In the post-genomic era, systems-level studies are being performed that seek to explain complex biological systems by integrating diverse resources from fields such as genomics, proteomics or transcriptomics. New information management systems are now needed for the collection, validation and analysis of the...
journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2006-06-23 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2007-11-30 00:00:00
abstract:BACKGROUND:T-cell epitopes that promiscuously bind to multiple alleles of a human leukocyte antigen (HLA) supertype are prime targets for development of vaccines and immunotherapies because they are relevant to a large proportion of the human population. The presence of clusters of promiscuous T-cell epitopes, immunolo...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-S1-S19
更新日期:2008-01-01 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2017-05-02 00:00:00
abstract:BACKGROUND:Sequence comparison is one of the most prominent tools in biological research, and is instrumental in studying gene function and evolution. The rapid development of high-throughput technologies for measuring protein interactions calls for extending this fundamental operation to the level of pathways in prote...
journal_title:BMC bioinformatics
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更新日期:2006-04-10 00:00:00
abstract:BACKGROUND:XHMM is a widely used tool for copy-number variant (CNV) discovery from whole exome sequencing data but can require hours to days to run for large cohorts. A more scalable implementation would reduce the need for specialized computational resources and enable increased exploration of the configuration parame...
journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2019-10-11 00:00:00
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pub_type: 杂志文章
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更新日期:2016-10-03 00:00:00
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更新日期:2013-07-24 00:00:00
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pub_type: 杂志文章
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更新日期:2015-10-22 00:00:00
abstract:BACKGROUND:Long short-term memory (LSTM) is one of the most attractive deep learning methods to learn time series or contexts of input data. Increasing studies, including biological sequence analyses in bioinformatics, utilize this architecture. Amino acid sequence profiles are widely used for bioinformatics studies, s...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2284-1
更新日期:2018-07-18 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2010-11-08 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2013-09-18 00:00:00
abstract:BACKGROUND:An important mechanism of endocrine activity is chemicals entering target cells via transport proteins and then interacting with hormone receptors such as the estrogen receptor (ER). α-Fetoprotein (AFP) is a major transport protein in rodent serum that can bind and sequester estrogens, thus preventing entry ...
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pub_type: 杂志文章
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更新日期:2013-01-01 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1790-x
更新日期:2017-09-13 00:00:00
abstract:BACKGROUND:One of the important goals in the post-genomic era is to determine the regulatory elements within the non-coding DNA of a given organism's genome. The identification of functional cis-regulatory modules has proven difficult since the component factor binding sites are small and the rules governing their arra...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-4-57
更新日期:2003-11-20 00:00:00
abstract:BACKGROUND:Computational discovery of transcription factor binding sites (TFBS) is a challenging but important problem of bioinformatics. In this study, improvement of a Gibbs sampling based technique for TFBS discovery is attempted through an approach that is widely known, but which has never been investigated before:...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-486
更新日期:2006-11-04 00:00:00
abstract:BACKGROUND:High-throughput sequencing can identify numerous potential genomic targets for microbial strain typing, but identification of the most informative combinations requires the use of computational screening tools. This paper describes novel software-- Automated Selection of Typing Target Subsets (AuSeTTS)--that...
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pub_type: 杂志文章
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更新日期:2013-05-01 00:00:00
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更新日期:2017-10-03 00:00:00
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pub_type: 临床试验,杂志文章
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更新日期:2019-02-28 00:00:00
abstract:BACKGROUND:The ability to detect nuclei in embryos is essential for studying the development of multicellular organisms. A system of automated nuclear detection has already been tested on a set of four-dimensional (4D) Nomarski differential interference contrast (DIC) microscope images of Caenorhabditis elegans embryos...
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pub_type: 杂志文章
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更新日期:2005-05-24 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-31
更新日期:2007-01-30 00:00:00
abstract:BACKGROUND:Endometrial cancers (ECs) are one of the most common types of malignant tumor in females. Substantial efforts had been made to identify significantly mutated genes (SMGs) in ECs and use them as biomarkers for the classification of histological subtypes and the prediction of clinical outcomes. However, the im...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1891-6
更新日期:2017-12-28 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:Structural variants (SVs) in human genomes are implicated in a variety of human diseases. Long-read sequencing delivers much longer read lengths than short-read sequencing and may greatly improve SV detection. However, due to the relatively high cost of long-read sequencing, it is unclear what coverage is ne...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2207-1
更新日期:2018-05-23 00:00:00
abstract:BACKGROUND:This paper addresses the prediction of the free energy of binding of a drug candidate with enzyme InhA associated with Mycobacterium tuberculosis. This problem is found within rational drug design, where interactions between drug candidates and target proteins are verified through molecular docking simulatio...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-310
更新日期:2012-11-21 00:00:00
abstract:BACKGROUND:The Gene Ontology is a controlled vocabulary for representing knowledge related to genes and proteins in a computable form. The current effort of manually annotating proteins with the Gene Ontology is outpaced by the rate of accumulation of biomedical knowledge in literature, which urges the development of t...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-525
更新日期:2008-12-08 00:00:00
abstract:BACKGROUND:Common existing phylogenetic tree visualisation tools are not able to display readable trees with more than a few thousand nodes. These existing methodologies are based in two dimensional space. RESULTS:We introduce the idea of visualising phylogenetic trees in three dimensional hyperbolic space with the Wa...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-5-48
更新日期:2004-04-29 00:00:00