The COG database: an updated version includes eukaryotes.

abstract：BACKGROUND:Proteins are dynamic molecules with motions ranging from picoseconds to longer than seconds. Many protein functions, however, appear to occur on the micro to millisecond timescale and therefore there has been intense research of the importance of these motions in catalysis and molecular interactions. Nuclear...

journal_title：BMC bioinformatics

authors： Bieri M,Gooley PR

更新日期：2011-10-27 00:00:00

abstract：BACKGROUND:Observed co-expression of a group of genes is frequently attributed to co-regulation by shared transcription factors. This assumption has led to the hypothesis that promoters of co-expressed genes should share common regulatory motifs, which forms the basis for numerous computational tools that search for th...

journal_title：BMC bioinformatics

authors： Meng G,Mosig A,Vingron M

更新日期：2010-05-20 00:00:00

abstract：BACKGROUND:Traditional algorithms for hidden Markov model decoding seek to maximize either the probability of a state path or the number of positions of a sequence assigned to the correct state. These algorithms provide only a single answer and in practice do not produce good results. RESULTS:We explore an alternative...

journal_title：BMC bioinformatics

authors： Brown DG,Golod D

更新日期：2010-01-18 00:00:00

abstract：BACKGROUND:We introduce a novel method, called PuFFIN, that takes advantage of paired-end short reads to build genome-wide nucleosome maps with larger numbers of detected nucleosomes and higher accuracy than existing tools. In contrast to other approaches that require users to optimize several parameters according to t...

journal_title：BMC bioinformatics

authors： Polishko A,Bunnik EM,Le Roch KG,Lonardi S

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:The goal of class prediction studies is to develop rules to accurately predict the class membership of new samples. The rules are derived using the values of the variables available for each subject: the main characteristic of high-dimensional data is that the number of variables greatly exceeds the number o...

journal_title：BMC bioinformatics

authors： Blagus R,Lusa L

更新日期：2010-10-20 00:00:00

abstract：BACKGROUND:The definition of a distance measure plays a key role in the evaluation of different clustering solutions of gene expression profiles. In this empirical study we compare different clustering solutions when using the Mutual Information (MI) measure versus the use of the well known Euclidean distance and Pears...

journal_title：BMC bioinformatics

authors： Priness I,Maimon O,Ben-Gal I

更新日期：2007-03-30 00:00:00

abstract：BACKGROUND:The evolutionary history of genes serves as a cornerstone of contemporary biology. Most conserved sequences in mammalian genomes don't code for proteins, yielding a need to infer evolutionary history of sequences irrespective of what kind of functional element they may encode. Thus, sequence-, as opposed to ...

journal_title：BMC bioinformatics

authors： Gao K,Miller J

更新日期：2020-02-06 00:00:00

abstract：BACKGROUND:Over the last decade, next generation sequencing (NGS) has become widely available, and is now the sequencing technology of choice for most researchers. Nonetheless, NGS presents a challenge for the evolutionary biologists who wish to estimate evolutionary genetic parameters from a mixed sample of unlabelled...

journal_title：BMC bioinformatics

authors： Wu SH,Rodrigo AG

更新日期：2015-11-04 00:00:00

abstract：BACKGROUND:Normalization in real-time qRT-PCR is necessary to compensate for experimental variation. A popular normalization strategy employs reference gene(s), which may introduce additional variability into normalized expression levels due to innate variation (between tissues, individuals, etc). To minimize this inna...

journal_title：BMC bioinformatics

authors： Chervoneva I,Li Y,Schulz S,Croker S,Wilson C,Waldman SA,Hyslop T

更新日期：2010-05-14 00:00:00

abstract：BACKGROUND:High-throughput sequencing has rapidly become an essential part of precision cancer medicine. But validating results obtained from analyzing and interpreting genomic data remains a rate-limiting factor. The gold standard, of course, remains manual validation by expert panels, which is not without its weaknes...

journal_title：BMC bioinformatics

authors： Bian X,Zhu B,Wang M,Hu Y,Chen Q,Nguyen C,Hicks B,Meerzaman D

更新日期：2018-11-19 00:00:00

abstract：BACKGROUND:A number of tools for the examination of linkage disequilibrium (LD) patterns between nearby alleles exist, but none are available for quickly and easily investigating LD at longer ranges (>500 kb). We have developed a web-based query tool (GLIDERS: Genome-wide LInkage DisEquilibrium Repository and Search en...

journal_title：BMC bioinformatics

authors： Lawrence R,Day-Williams AG,Mott R,Broxholme J,Cardon LR,Zeggini E

更新日期：2009-10-31 00:00:00

abstract：BACKGROUND:Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for computational purposes. Funding for further development of the Complex Carboh...

journal_title：BMC bioinformatics

authors： Ranzinger R,Herget S,Wetter T,von der Lieth CW

更新日期：2008-09-19 00:00:00

abstract：BACKGROUND:Over the last two decades, an innovative technology called Tissue Microarray (TMA), which combines multi-tissue and DNA microarray concepts, has been widely used in the field of histology. It consists of a collection of several (up to 1000 or more) tissue samples that are assembled onto a single support - ty...

journal_title：BMC bioinformatics

authors： Nguyen HN,Paveau V,Cauchois C,Kervrann C

更新日期：2018-04-19 00:00:00

abstract：BACKGROUND:Advances in sequencing and genotyping technologies are leading to the widespread availability of multi-species variation data, dense genotype data and large-scale resequencing projects. The 1000 Genomes Project and similar efforts in other species are challenging the methods previously used for storage and m...

journal_title：BMC bioinformatics

authors： Rios D,McLaren WM,Chen Y,Birney E,Stabenau A,Flicek P,Cunningham F

更新日期：2010-05-11 00:00:00

abstract：BACKGROUND:In bioinformatics community, many tasks associate with matching a set of protein query sequences in large sequence datasets. To conduct multiple queries in the database, a common used method is to run BLAST on each original querey or on the concatenated queries. It is inefficient since it doesn't exploit the...

journal_title：BMC bioinformatics

authors： Ge H,Sun L,Yu J

更新日期：2017-11-21 00:00:00

abstract：BACKGROUND:Comparative analysis of whole genome sequence data from closely related prokaryotic species or strains is becoming an increasingly important and accessible approach for addressing both fundamental and applied biological questions. While there are number of excellent tools developed for performing this task, ...

journal_title：BMC bioinformatics

authors： Thakur S,Guttman DS

更新日期：2016-06-30 00:00:00

abstract：BACKGROUND:Genome imputation, admixture resolution and genome-wide association analyses are timely and computationally intensive processes with many composite and requisite steps. Analysis time increases further when building and installing the run programs required for these analyses. For scientists that may not be as...

journal_title：BMC bioinformatics

authors： Eller RJ,Janga SC,Walsh S

更新日期：2019-06-28 00:00:00

abstract：BACKGROUND:Gene expression microarray experiments are expensive to conduct and guidelines for acceptable quality control at intermediate steps before and after the samples are hybridised to chips are vague. We conducted an experiment hybridising RNA from human brain to 117 U133A Affymetrix GeneChips and used these data...

journal_title：BMC bioinformatics

authors： Jones L,Goldstein DR,Hughes G,Strand AD,Collin F,Dunnett SB,Kooperberg C,Aragaki A,Olson JM,Augood SJ,Faull RL,Luthi-Carter R,Moskvina V,Hodges AK

更新日期：2006-04-19 00:00:00

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

authors： Dubinkina VB,Ischenko DS,Ulyantsev VI,Tyakht AV,Alexeev DG

更新日期：2016-01-16 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

authors： Varón A,Wheeler WC

更新日期：2013-02-26 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

authors： Kong W,Mou X,Hu X

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:Selective pressures at the DNA level shape genes into profiles consisting of patterns of rapidly evolving sites and sites withstanding change. These profiles remain detectable even when protein sequences become extensively diverged. A common task in molecular biology is to infer functional, structural or evo...

journal_title：BMC bioinformatics

authors： Ndhlovu A,Hazelhurst S,Durand PM

更新日期：2015-08-14 00:00:00

abstract：BACKGROUND:Since proteins perform their functions by interacting with one another and with other biomolecules, reconstructing a map of the protein-protein interactions of a cell, experimentally or computationally, is an important first step toward understanding cellular function and machinery of a proteome. Solely deri...

journal_title：BMC bioinformatics

authors： Wu X,Zhu L,Guo J,Fu C,Zhou H,Dong D,Li Z,Zhang DY,Lin K

更新日期：2006-12-18 00:00:00

abstract：BACKGROUND:In recent years, a considerable amount of research effort has been directed to the analysis of biological networks with the availability of genome-scale networks of genes and/or proteins of an increasing number of organisms. A protein-protein interaction (PPI) network is a particular biological network which...

journal_title：BMC bioinformatics

authors： Turanalp ME,Can T

更新日期：2008-06-11 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

authors： Kerr KF

更新日期：2007-10-03 00:00:00

abstract：: ...

journal_title：BMC bioinformatics

authors： Wren JD,Doerkson RJ,Toby IT,Nanduri B,Homayouni R,Manda P,Thakkar S

更新日期：2019-03-14 00:00:00

abstract：BACKGROUND:Historically, two categories of computational algorithms (alignment-based and alignment-free) have been applied to sequence comparison-one of the most fundamental issues in bioinformatics. Multiple sequence alignment, although dominantly used by biologists, possesses both fundamental as well as computational...

journal_title：BMC bioinformatics

authors： Lu G,Zhang S,Fang X

更新日期：2008-05-28 00:00:00

abstract：BACKGROUND:Many proteins contain conserved sequence patterns (motifs) that contribute to their functionality. The process of experimentally identifying and validating novel protein motifs can be difficult, expensive, and time consuming. A means for helping to identify in advance the possible function of a novel motif i...

journal_title：BMC bioinformatics

authors： Bristow F,He R,Van Domselaar G

更新日期：2011-09-26 00:00:00

abstract：BACKGROUND:The Codon Adaptation Index (CAI) is a measure of the synonymous codon usage bias for a DNA or RNA sequence. It quantifies the similarity between the synonymous codon usage of a gene and the synonymous codon frequency of a reference set. Extreme values in the nucleotide or in the amino acid composition have a...

journal_title：BMC bioinformatics

authors： Puigbò P,Bravo IG,Garcia-Vallvé S

更新日期：2008-01-29 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

authors： Oberto J

更新日期：2010-11-11 00:00:00