Abstract:
BACKGROUND:A new algorithm has been developed for generating conservation profiles that reflect the evolutionary history of the subfamily associated with a query sequence. It is based on n-gram patterns (NP{n,m}) which are sets of n residues and m wildcards in windows of size n+m. The generation of conservation profiles is treated as a signal-to-noise problem where the signal is the count of n-gram patterns in target sequences that are similar to the query sequence and the noise is the count over all target sequences. The signal is differentiated from the noise by applying singular value decomposition to sets of target sequences rank ordered by similarity with respect to the query. RESULTS:The new algorithm was used to construct 4,248 profiles from 120 randomly selected Pfam-A families. These were compared to profiles generated from multiple alignments using the consensus approach. The two profiles were similar whenever the subfamily associated with the query sequence was well represented in the multiple alignment. It was possible to construct subfamily specific conservation profiles using the new algorithm for subfamilies with as few as five members. The speed of the new algorithm was comparable to the multiple alignment approach. CONCLUSION:Subfamily specific conservation profiles can be generated by the new algorithm without aprioi knowledge of family relationships or domain architecture. This is useful when the subfamily contains multiple domains with different levels of representation in protein databases. It may also be applicable when the subfamily sample size is too small for the multiple alignment approach.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Vries JK,Liu Xdoi
10.1186/1471-2105-9-72subject
Has Abstractpub_date
2008-01-30 00:00:00pages
72issn
1471-2105pii
1471-2105-9-72journal_volume
9pub_type
杂志文章abstract:BACKGROUND:Identifying differentially abundant features between different experimental groups is a common goal for many metabolomics and proteomics studies. However, analyzing data from mass spectrometry (MS) is difficult because the data may not be normally distributed and there is often a large fraction of zero value...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3067-z
更新日期:2019-10-17 00:00:00
abstract:BACKGROUND:Normalization is the process of removing non-biological sources of variation between array experiments. Recent investigations of data in gene expression databases for varying organisms and tissues have shown that the majority of expressed genes exhibit a power-law distribution with an exponent close to -1 (i...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-37
更新日期:2005-02-23 00:00:00
abstract:BACKGROUND:Conservation and variation scores are used when evaluating sites in a multiple sequence alignment, in order to identify residues critical for structure or function. A variety of scores are available today but it is not clear how different scores relate to each other. RESULTS:We applied 25 conservation and v...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-388
更新日期:2010-07-21 00:00:00
abstract:BACKGROUND:Finding common molecular interactions from different samples is essential work to understanding diseases and other biological processes. Coexpression networks and their modules directly reflect sample-specific interactions among genes. Therefore, identification of common coexpression network or modules may r...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2193-3
更新日期:2018-06-13 00:00:00
abstract:BACKGROUND:The Bacteria Biotope (BB) task is a biomedical relation extraction (RE) that aims to study the interaction between bacteria and their locations. This task is considered to pertain to fundamental knowledge in applied microbiology. Some previous investigations conducted the study by applying feature-based mode...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3217-3
更新日期:2019-12-03 00:00:00
abstract:BACKGROUND:A phylogeny postulates shared ancestry relationships among organisms in the form of a binary tree. Phylogenies attempt to answer an important question posed in biology: what are the ancestor-descendent relationships between organisms? At the core of every biological problem lies a phylogenetic component. The...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-66
更新日期:2013-02-26 00:00:00
abstract::Following last year's computational vaccinology workshop in Shanghai, China, the third ISV Pre-conference Computational Vaccinology Workshop (ICoVax 2013) was held in Barcelona, Spain. ICoVax 2013 provided an international platform for the attendees to showcase their research and discuss problems and solutions in the ...
journal_title:BMC bioinformatics
pub_type:
doi:10.1186/1471-2105-15-S4-I1
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:SSWAP (Simple Semantic Web Architecture and Protocol; pronounced "swap") is an architecture, protocol, and platform for using reasoning to semantically integrate heterogeneous disparate data and services on the web. SSWAP was developed as a hybrid semantic web services technology to overcome limitations foun...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-309
更新日期:2009-09-23 00:00:00
abstract:BACKGROUND:Bioinformatics software quality assurance is essential in genomic medicine. Systematic verification and validation of bioinformatics software is difficult because it is often not possible to obtain a realistic "gold standard" for systematic evaluation. Here we apply a technique that originates from the softw...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-S16-S15
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:The advance of next generation sequencing enables higher throughput with lower price, and as the basic of high-throughput sequencing data analysis, variant calling is widely used in disease research, clinical treatment and medicine research. However, current mainstream variant caller tools have a serious pro...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-2665-0
更新日期:2019-02-14 00:00:00
abstract:BACKGROUND:Sequence mutations represent a driving force of adaptive evolution in bacterial pathogens. It is especially evident in reductive genome evolution where bacteria underwent lifestyles shifting from a free-living to a strictly intracellular or host-depending life. It resulted in loss-of-function mutations and/o...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-S1-S3
更新日期:2009-01-30 00:00:00
abstract:BACKGROUND:Guide-trees are used as part of an essential heuristic to enable the calculation of multiple sequence alignments. They have been the focus of much method development but there has been little effort at determining systematically, which guide-trees, if any, give the best alignments. Some guide-tree constructi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-338
更新日期:2014-10-04 00:00:00
abstract:BACKGROUND:Creating a scalable computational infrastructure to analyze the wealth of information contained in data repositories is difficult due to significant barriers in organizing, extracting and analyzing relevant data. Shared data science infrastructures like Boag is needed to efficiently process and parse data co...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-2967-2
更新日期:2019-08-22 00:00:00
abstract:BACKGROUND:The PathoLogic program constructs Pathway/Genome databases by using a genome's annotation to predict the set of metabolic pathways present in an organism. PathoLogic determines the set of reactions composing those pathways from the enzymes annotated in the organism's genome. Most annotation efforts fail to a...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-5-76
更新日期:2004-06-09 00:00:00
abstract:BACKGROUND:The frequent exchange of genetic material among prokaryotes means that extracting a majority or plurality phylogenetic signal from many gene families, and the identification of gene families that are in significant conflict with the plurality signal is a frequent task in comparative genomics, and especially ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-123
更新日期:2012-06-07 00:00:00
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
doi:10.1186/1471-2105-7-318
更新日期:2006-06-23 00:00:00
abstract:BACKGROUND:Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of seque...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-186
更新日期:2008-04-10 00:00:00
abstract:BACKGROUND:Identification of expression quantitative trait loci (eQTLs) is an emerging area in genomic study. The task requires an integrated analysis of genome-wide single nucleotide polymorphism (SNP) data and gene expression data, raising a new computational challenge due to the tremendous size of data. RESULTS:We ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-S9-S2
更新日期:2010-10-28 00:00:00
abstract:BACKGROUND:Microsatellite (simple sequence repeat - SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic research projects require high-throughput computer-assisted primer design. Numerous such web-based or ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-253
更新日期:2008-05-29 00:00:00
abstract:BACKGROUND:DNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations. RESULTS:Here, we describe a method to detect copy number varia...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-80
更新日期:2009-03-06 00:00:00
abstract:BACKGROUND:Identifying diagnosis and prognosis biomarkers from expression profiling data is of great significance for achieving personalized medicine and designing therapeutic strategy in complex diseases. However, the reproducibility of identified biomarkers across tissues and experiments is still a challenge for this...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0519-y
更新日期:2015-03-18 00:00:00
abstract:BACKGROUND:Molecular biology data exist on diverse scales, from the level of molecules to -omics. At the same time, the data at each scale can be categorised into multiple layers, such as the genome, transcriptome, proteome, metabolome, and biochemical pathways. Due to the highly multi-layer and multi-dimensional natur...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-31
更新日期:2009-01-23 00:00:00
abstract:BACKGROUND:Abundant information about gene products is stored in online searchable databases such as annotation or literature. To efficiently obtain and digest such information, there is a pressing need for automated information-summarization and functional-similarity clustering of genes. RESULTS:We have developed a n...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-392
更新日期:2006-08-29 00:00:00
abstract:BACKGROUND:The binding of regulatory proteins to their specific DNA targets determines the accurate expression of the neighboring genes. The in silico prediction of new binding sites in completely sequenced genomes is a key aspect in the deeper understanding of gene regulatory networks. Several algorithms have been des...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-554
更新日期:2010-11-11 00:00:00
abstract:BACKGROUND:The inference of homology between proteins is a key problem in molecular biology The current best approaches only identify approximately 50% of homologies (with a false positive rate set at 1/1000). RESULTS:We present Homology Induction (HI), a new approach to inferring homology. HI uses machine learning to...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-3-11
更新日期:2002-04-23 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:Protein-protein interactions (PPIs) play several roles in living cells, and computational PPI prediction is a major focus of many researchers. The three-dimensional (3D) structure and binding surface are important for the design of PPI inhibitors. Therefore, rigid body protein-protein docking calculations fo...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2073-x
更新日期:2018-05-08 00:00:00
abstract:BACKGROUND:The MAQC project demonstrated that microarrays with comparable content show inter- and intra-platform reproducibility. However, since the content of gene databases still increases, the development of new generations of microarrays covering new content is mandatory. To better understand the potential challeng...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-186
更新日期:2009-06-18 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:Microarray devices permit a genome-scale evaluation of gene function. This technology has catalyzed biomedical research and development in recent years. As many important diseases can be traced down to the gene level, a long-standing research problem is to identify specific gene expression patterns linking t...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-67
更新日期:2005-03-22 00:00:00