NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly.

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

authors： Bozdag S,Close TJ,Lonardi S

更新日期：2009-07-15 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

authors： You FM,Huo N,Gu YQ,Luo MC,Ma Y,Hane D,Lazo GR,Dvorak J,Anderson OD

更新日期：2008-05-29 00:00:00

abstract：BACKGROUND:Although methods based on highly abstract descriptions of protein structures, such as VAST and TOPS, can perform very fast protein structure comparison, the results can lack a high degree of biological significance. Previously we have discussed the basic mechanisms of our novel method for structure compariso...

journal_title：BMC bioinformatics

authors： Veeramalai M,Gilbert D,Valiente G

更新日期：2010-03-17 00:00:00

abstract：BACKGROUND:A standardized and cost-effective molecular identification system is now an urgent need for Fungi owing to their wide involvement in human life quality. In particular the potential use of mitochondrial DNA species markers has been taken in account. Unfortunately, a serious difficulty in the PCR and bioinform...

journal_title：BMC bioinformatics

authors： Santamaria M,Vicario S,Pappadà G,Scioscia G,Scazzocchio C,Saccone C

更新日期：2009-06-16 00:00:00

abstract：BACKGROUND:The detection of bias due to cryptic population structure is an important step in the evaluation of findings of genetic association studies. The standard method of measuring this bias in a genetic association study is to compare the observed median association test statistic to the expected median test stati...

journal_title：BMC bioinformatics

authors： Pirie A,Wood A,Lush M,Tyrer J,Pharoah PD

更新日期：2015-02-20 00:00:00

abstract：BACKGROUND:X-converting enzyme (XCE) involved in nervous control of respiration, is a member of the M13 family of zinc peptidases, for which no natural substrate has been identified yet. In contrast, it's well characterized homologue endothelin-converting enzyme-1 (ECE-1) showed broad substrate specificity and acts as ...

journal_title：BMC bioinformatics

authors： Ul-Haq Z,Iqbal S,Moin ST

更新日期：2012-11-01 00:00:00

abstract：BACKGROUND:The large gap between the number of protein sequences in databases and the number of functionally characterized proteins calls for the development of a fast computational tool for the prediction of subnuclear and subcellular localizations generally applicable to protein sequences. The information on localiza...

journal_title：BMC bioinformatics

authors： Lei Z,Dai Y

更新日期：2005-12-07 00:00:00

abstract：BACKGROUND:SNP genotyping microarrays have revolutionized the study of complex disease. The current range of commercially available genotyping products contain extensive catalogues of low frequency and rare variants. Existing SNP calling algorithms have difficulty dealing with these low frequency variants, as the under...

journal_title：BMC bioinformatics

authors： Liu R,Dai Z,Yeager M,Irizarry RA,Ritchie ME

更新日期：2014-05-23 00:00:00

abstract：BACKGROUND:The adaptation of the CRISPR-Cas9 system to pooled library gene knockout screens in mammalian cells represents a major technological leap over RNA interference, the prior state of the art. New methods for analyzing the data and evaluating results are needed. RESULTS:We offer BAGEL (Bayesian Analysis of Gene...

journal_title：BMC bioinformatics

authors： Hart T,Moffat J

更新日期：2016-04-16 00:00:00

abstract：BACKGROUND:De novo assembly of RNA-seq data allows the study of transcriptome in absence of a reference genome either if data is obtained from a single organism or from a mixed sample as in metatranscriptomics studies. Given the high number of sequences obtained from NGS approaches, a critical step in any analysis work...

journal_title：BMC bioinformatics

authors： Saggese I,Bona E,Conway M,Favero F,Ladetto M,Liò P,Manzini G,Mignone F

更新日期：2018-07-09 00:00:00

abstract：BACKGROUND:Although it is not difficult for state-of-the-art gene finders to identify coding regions in prokaryotic genomes, exact prediction of the corresponding translation initiation sites (TIS) is still a challenging problem. Recently a number of post-processing tools have been proposed for improving the annotation...

journal_title：BMC bioinformatics

authors： Tech M,Meinicke P

更新日期：2006-03-09 00:00:00

abstract：BACKGROUND:Although many of the genic features in Mycobacterium abscessus have been fully validated, a comprehensive understanding of the regulatory elements remains lacking. Moreover, there is little understanding of how the organism regulates its transcriptomic profile, enabling cells to survive in hostile environmen...

journal_title：BMC bioinformatics

authors： Staunton PM,Miranda-CasoLuengo AA,Loftus BJ,Gormley IC

更新日期：2019-09-10 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

authors： Jin B,Muller B,Zhai C,Lu X

更新日期：2008-12-08 00:00:00

abstract：BACKGROUND:Structural alignment of proteins is one of the most challenging problems in molecular biology. The tertiary structure of a protein strictly correlates with its function and computationally predicted structures are nowadays a main premise for understanding the latter. However, computationally derived 3D model...

journal_title：BMC bioinformatics

authors： Antczak M,Kasprzak M,Lukasiak P,Blazewicz J

更新日期：2016-09-17 00:00:00

abstract：BACKGROUND:Maturation inhibitors are a new class of antiretroviral drugs. Bevirimat (BVM) was the first substance in this class of inhibitors entering clinical trials. While the inhibitory function of BVM is well established, the molecular mechanisms of action and resistance are not well understood. It is known that mu...

journal_title：BMC bioinformatics

authors： Heider D,Verheyen J,Hoffmann D

更新日期：2010-01-20 00:00:00

abstract：BACKGROUND:Biological molecules are often asymmetric with respect to stereochemistry, and correct stereochemistry is essential to their function. Molecular dynamics simulations of biomolecules have increasingly become an integral part of biophysical research. However, stereochemical errors in biomolecular structures ca...

journal_title：BMC bioinformatics

authors： Schreiner E,Trabuco LG,Freddolino PL,Schulten K

更新日期：2011-05-23 00:00:00

abstract：BACKGROUND:Failure on Highly Active Anti-Retroviral Treatment is often accompanied with development of antiviral resistance to one or more drugs included in the treatment. In general, the virus is more likely to develop resistance to drugs with a lower genetic barrier. Previously, we developed a method to reverse engin...

journal_title：BMC bioinformatics

authors： Theys K,Deforche K,Beheydt G,Moreau Y,van Laethem K,Lemey P,Camacho RJ,Rhee SY,Shafer RW,Van Wijngaerden E,Vandamme AM

更新日期：2010-08-03 00:00:00

abstract：BACKGROUND:An increasing number of researchers have released novel RNA structure analysis and prediction algorithms for comparative approaches to structure prediction. Yet, independent benchmarking of these algorithms is rarely performed as is now common practice for protein-folding, gene-finding and multiple-sequence-...

journal_title：BMC bioinformatics

authors： Gardner PP,Giegerich R

更新日期：2004-09-30 00:00:00

abstract：BACKGROUND:Comprehensive two-dimensional gas chromatography coupled with mass spectrometry (GC × GC-MS) is a powerful technique which has gained increasing attention over the last two decades. The GC × GC-MS provides much increased separation capacity, chemical selectivity and sensitivity for complex sample analysis an...

journal_title：BMC bioinformatics

authors： Kim S,Koo I,Fang A,Zhang X

更新日期：2011-06-15 00:00:00

abstract：BACKGROUND:Global maritime trade plays an important role in the modern transportation industry. It brings significant economic profit along with bioinvasion risk. Species translocate and establish in a non-native area through ballast water and biofouling. Aiming at aquatic bioinvasion issue, people proposed various sug...

journal_title：BMC bioinformatics

authors： Wang S,Wang C,Wang S,Ma L

更新日期：2018-08-13 00:00:00

abstract：BACKGROUND:Mecp2 null mice model Rett syndrome (RTT) a human neurological disorder affecting females after apparent normal pre- and peri-natal developmental periods. Neuroanatomical studies in cerebral cortex of RTT mouse models revealed delayed maturation of neuronal morphology and autonomous as well as non-cell auton...

journal_title：BMC bioinformatics

authors： Vacca M,Tripathi KP,Speranza L,Aiese Cigliano R,Scalabrì F,Marracino F,Madonna M,Sanseverino W,Perrone-Capano C,Guarracino MR,D'Esposito M

更新日期：2016-01-20 00:00:00

abstract：BACKGROUND:As phenotypic features derived from heritable characters, the topologies of metabolic pathways contain both phylogenetic and phenetic components. In the post-genomic era, it is possible to measure the "phylophenetic" contents of different pathways topologies from a global perspective. RESULTS:We reconstruct...

journal_title：BMC bioinformatics

authors： Zhang Y,Li S,Skogerbø G,Zhang Z,Zhu X,Zhang Z,Sun S,Lu H,Shi B,Chen R

更新日期：2006-05-09 00:00:00

abstract：BACKGROUND:The analysis of mass spectra suggests that the existence of derivative peaks is strongly dependent on the intensity of the primary peaks. Peak selection from tandem mass spectrum is used to filter out noise and contaminant peaks. It is widely accepted that a valid primary peak tends to have high intensity an...

journal_title：BMC bioinformatics

authors： Zhang S,Wang Y,Bu D,Zhang H,Sun S

更新日期：2011-08-17 00:00:00

abstract：BACKGROUND:The rapid pace of bioscience research makes it very challenging to track relevant articles in one's area of interest. MEDLINE, a primary source for biomedical literature, offers access to more than 20 million citations with three-quarters of a million new ones added each year. Thus it is not surprising to se...

journal_title：BMC bioinformatics

authors： Srinivasan P,Zhang XN,Bouten R,Chang C

更新日期：2015-06-20 00:00:00

abstract：BACKGROUND:Current microRNA (miRNA) research in progress has engendered rapid accumulation of expression data evolving from microarray experiments. Such experiments are generally performed over different tissues belonging to a specific species of metazoan. For disease diagnosis, microarray probes are also prepared with...

journal_title：BMC bioinformatics

authors： Bandyopadhyay S,Bhattacharyya M

更新日期：2009-05-28 00:00:00

abstract：BACKGROUND:Biological sequences play a major role in molecular and computational biology. They are studied as information-bearing entities that make up DNA, RNA or proteins. The Sequence Ontology, which is part of the OBO Foundry, contains descriptions and definitions of sequences and their properties. Yet the most bas...

journal_title：BMC bioinformatics

authors： Hoehndorf R,Kelso J,Herre H

更新日期：2009-11-18 00:00:00

abstract：BACKGROUND:Proton Magnetic Resonance (MR) Spectroscopy (MRS) is a widely available technique for those clinical centres equipped with MR scanners. Unlike the rest of MR-based techniques, MRS yields not images but spectra of metabolites in the tissues. In pathological situations, the MRS profile changes and this has bee...

journal_title：BMC bioinformatics

authors： Pérez-Ruiz A,Julià-Sapé M,Mercadal G,Olier I,Majós C,Arús C

更新日期：2010-11-29 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:Alternative splicing is a major contributor to the diversity of eukaryotic transcriptomes and proteomes. Currently, large scale detection of alternative splicing using expressed sequence tags (ESTs) or microarrays does not capture all alternative splicing events. Moreover, for many species genomic data is be...

journal_title：BMC bioinformatics

authors： Sinha R,Hiller M,Pudimat R,Gausmann U,Platzer M,Backofen R

更新日期：2008-11-12 00:00:00

abstract：BACKGROUND:The locations and shapes of synapses are important in reconstructing connectomes and analyzing synaptic plasticity. However, current synapse detection and segmentation methods are still not adequate for accurately acquiring the synaptic connectivity, and they cannot effectively alleviate the burden of synaps...

journal_title：BMC bioinformatics

authors： Xiao C,Li W,Deng H,Chen X,Yang Y,Xie Q,Han H

更新日期：2018-07-13 00:00:00