MapMi: automated mapping of microRNA loci.

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:Protein function is closely intertwined with protein structure. Discovery of meaningful structure-function relationships is of utmost importance in protein biochemistry and has led to creation of high-quality, manually curated classification databases, such as the gold-standard SCOP (Structural Classificatio...

journal_title：BMC bioinformatics

authors： Asarnow D,Singh R

更新日期：2014-01-01 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:Hidden variability is a fundamentally important issue in the context of gene expression studies. Collected tissue samples may have a wide variety of hidden effects that may alter their transcriptional landscape significantly. As a result their actual differential expression pattern can be potentially distort...

journal_title：BMC bioinformatics

authors： Chakraborty S,Datta S,Datta S

更新日期：2013-07-24 00:00:00

abstract：BACKGROUND:A cross-correlation (XCorr) score function is one of the most popular score functions utilized to search peptide identifications in databases, and many computer programs, such as SEQUEST, Comet, and Tide, currently use this score function. Recently, the HiXCorr algorithm was developed to speed up this score ...

journal_title：BMC bioinformatics

authors： Kim H,Han S,Um JH,Park K

更新日期：2018-12-12 00:00:00

abstract：BACKGROUND:Protein sequence motifs are by definition short fragments of conserved amino acids, often associated with a specific function. Accordingly protein sequence profiles derived from multiple sequence alignments provide an alternative description of functional motifs characterizing families of related sequences. ...

journal_title：BMC bioinformatics

authors： Hummel J,Keshvari N,Weckwerth W,Selbig J

更新日期：2005-06-29 00:00:00

abstract：BACKGROUND:The increasing availability of Electronic Health Record (EHR) data and specifically free-text patient notes presents opportunities for phenotype extraction. Text-mining methods in particular can help disease modeling by mapping named-entities mentions to terminologies and clustering semantically related term...

journal_title：BMC bioinformatics

authors： Cohen R,Elhadad M,Elhadad N

更新日期：2013-01-16 00:00:00

abstract：BACKGROUND:RNA-seq is a powerful tool for measuring transcriptomes, especially for identifying differentially expressed genes or transcripts (DEGs) between sample groups. A number of methods have been developed for this task, and several evaluation studies have also been reported. However, those evaluations so far have...

journal_title：BMC bioinformatics

authors： Tang M,Sun J,Shimizu K,Kadota K

更新日期：2015-11-04 00:00:00

abstract：BACKGROUND:Tight clustering arose recently from a desire to obtain tighter and potentially more informative clusters in gene expression studies. Scattered genes with relatively loose correlations should be excluded from the clusters. However, in the literature there is little work dedicated to this area of research. On...

journal_title：BMC bioinformatics

authors： Yuan Y,Li CT,Wilson R

更新日期：2008-06-18 00:00:00

abstract：BACKGROUND:Typical evolutionary events like recombination, hybridization or gene transfer make necessary the use of phylogenetic networks to properly depict the evolution of DNA and protein sequences. Although several theoretical classes have been proposed to characterize these networks, they make stringent assumptions...

journal_title：BMC bioinformatics

authors： Arenas M,Patricio M,Posada D,Valiente G

更新日期：2010-05-20 00:00:00

abstract：BACKGROUND:Next (second) generation sequencing is an increasingly important tool for many areas of molecular biology, however, care must be taken when interpreting its output. Even a low error rate can cause a large number of errors due to the high number of nucleotides being sequenced. Identifying sequencing errors fr...

journal_title：BMC bioinformatics

authors： Sleep JA,Schreiber AW,Baumann U

更新日期：2013-12-18 00:00:00

abstract：BACKGROUND:The Damerau-Levenshtein (DL) distance metric has been widely used in the biological science. It tries to identify the similar region of DNA,RNA and protein sequences by transforming one sequence to the another using the substitution, insertion, deletion and transposition operations. Lowrance and Wagner have ...

journal_title：BMC bioinformatics

authors： Zhao C,Sahni S

更新日期：2020-12-09 00:00:00

abstract：BACKGROUND:The analysis of DNA copy number variants (CNV) has increasing impact in the field of genetic diagnostics and research. However, the interpretation of CNV data derived from high resolution array CGH or NGS platforms is complicated by the considerable variability of the human genome. Therefore, tools for multi...

journal_title：BMC bioinformatics

authors： Tebel K,Boldt V,Steininger A,Port M,Ebert G,Ullmann R

更新日期：2017-01-06 00:00:00

abstract：BACKGROUND:The toxic effects of many simple organic compounds stem from their biotransformation to chemically reactive metabolites which bind covalently to cellular proteins. To understand the mechanisms of cytotoxic responses it may be important to know which proteins become adducted and whether some may be common tar...

journal_title：BMC bioinformatics

authors： Hanzlik RP,Koen YM,Theertham B,Dong Y,Fang J

更新日期：2007-03-16 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

authors： Giannoulatou E,Park SH,Humphreys DT,Ho JW

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Protein subcellular localization is crucial for genome annotation, protein function prediction, and drug discovery. Determination of subcellular localization using experimental approaches is time-consuming; thus, computational approaches become highly desirable. Extensive studies of localization prediction h...

journal_title：BMC bioinformatics

authors： Su EC,Chiu HS,Lo A,Hwang JK,Sung TY,Hsu WL

更新日期：2007-09-08 00:00:00

abstract：BACKGROUND:Recently differential variability has been showed to be valuable in evaluating the association of DNA methylation to the risks of complex human diseases. The statistical tests based on both differential methylation level and differential variability can be more powerful than those based only on differential ...

journal_title：BMC bioinformatics

authors： Li X,Fu Y,Wang X,Qiu W

更新日期：2018-05-18 00:00:00

abstract：BACKGROUND:Protein function in eukaryotic cells is often controlled in a cell cycle-dependent manner. Therefore, the correct assignment of cellular phenotypes to cell cycle phases is a crucial task in cell biology research. Nuclear proteins whose localization varies during the cell cycle are valuable and frequently use...

journal_title：BMC bioinformatics

authors： Schönenberger F,Deutzmann A,Ferrando-May E,Merhof D

更新日期：2015-05-29 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

authors： Angelini C,De Canditiis D,De Feis I

更新日期：2014-05-09 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

authors： Gessler DD,Schiltz GS,May GD,Avraham S,Town CD,Grant D,Nelson RT

更新日期：2009-09-23 00:00:00

abstract：BACKGROUND:The nucleosome is the fundamental packing unit of DNAs in eukaryotic cells. Its detailed positioning on the genome is closely related to chromosome functions. Increasing evidence has shown that genomic DNA sequence itself is highly predictive of nucleosome positioning genome-wide. Therefore a fast software t...

journal_title：BMC bioinformatics

authors： Xi L,Fondufe-Mittendorf Y,Xia L,Flatow J,Widom J,Wang JP

更新日期：2010-06-24 00:00:00

abstract：BACKGROUND:Although both conservation and correlated mutation (CM) are important information reflecting the different sorts of context in multiple sequence alignment, most of alignment methods use sequence profiles that only represent conservation. There is no general way to represent correlated mutation and incorporat...

journal_title：BMC bioinformatics

authors： Jeong CS,Kim D

更新日期：2010-04-16 00:00:00

abstract：BACKGROUND:Bacterial pan-genomes, comprised of conserved and variable genes across multiple sequenced bacterial genomes, allow for identification of genomic regions that are phylogenetically discriminating or functionally important. Pan-genomes consist of large amounts of data, which can restrict researchers ability to...

journal_title：BMC bioinformatics

authors： Clarke TH,Brinkac LM,Inman JM,Sutton G,Fouts DE

更新日期：2018-06-27 00:00:00

abstract：BACKGROUND:Structural models determined by X-ray crystallography play a central role in understanding protein-protein interactions at the molecular level. Interpretation of these models requires the distinction between non-specific crystal packing contacts and biologically relevant interactions. This has been investiga...

journal_title：BMC bioinformatics

authors： Zhu H,Domingues FS,Sommer I,Lengauer T

更新日期：2006-01-19 00:00:00

abstract：BACKGROUND:Heritability of a phenotypic or molecular trait measures the proportion of variance that is attributable to genotypic variance. It is an important concept in breeding and genetics. Few methods are available for calculating heritability for traits derived from high-throughput sequencing. RESULTS:We propose s...

journal_title：BMC bioinformatics

authors： Rudra P,Shi WJ,Vestal B,Russell PH,Odell A,Dowell RD,Radcliffe RA,Saba LM,Kechris K

更新日期：2017-03-02 00:00:00

abstract：BACKGROUND:New sequencing techniques require new visualization strategies, as is the case for epigenomics data such as DNA base modifications, small non-coding RNAs, and histone modifications. RESULTS:We present a set of plugins for the genome browser JBrowse that are targeted for epigenomics visualizations. Specifica...

journal_title：BMC bioinformatics

authors： Hofmeister BT,Schmitz RJ

更新日期：2018-04-25 00:00:00

abstract：BACKGROUND:Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run a...

journal_title：BMC bioinformatics

authors： de Knikker R,Guo Y,Li JL,Kwan AK,Yip KY,Cheung DW,Cheung KH

更新日期：2004-03-10 00:00:00

abstract：BACKGROUND:With the growing availability of full-text articles online, scientists and other consumers of the life sciences literature now have the ability to go beyond searching bibliographic records (title, abstract, metadata) to directly access full-text content. Motivated by this emerging trend, I posed the followin...

journal_title：BMC bioinformatics

authors： Lin J

更新日期：2009-02-03 00:00:00

abstract：BACKGROUND:The landscape of biological and biomedical research is being changed rapidly with the invention of microarrays which enables simultaneous view on the transcription levels of a huge number of genes across different experimental conditions or time points. Using microarray data sets, clustering algorithms have ...

journal_title：BMC bioinformatics

authors： Maulik U,Mukhopadhyay A,Bandyopadhyay S

更新日期：2009-01-20 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