The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation.

abstract：BACKGROUND:It is possible to predict whether a tuberculosis (TB) patient will fail to respond to specific antibiotics by sequencing the genome of the infecting Mycobacterium tuberculosis (Mtb) and observing whether the pathogen carries specific mutations at drug-resistance sites. This advancement has led to the collati...

journal_title：BMC bioinformatics

authors： Ngo TM,Teo YY

更新日期：2019-02-08 00:00:00

abstract：BACKGROUND:The NTF2-like superfamily is a versatile group of protein domains sharing a common fold. The sequences of these domains are very diverse and they share no common sequence motif. These domains serve a range of different functions within the proteins in which they are found, including both catalytic and non-ca...

journal_title：BMC bioinformatics

authors： Eberhardt RY,Chang Y,Bateman A,Murzin AG,Axelrod HL,Hwang WC,Aravind L

更新日期：2013-11-19 00:00:00

abstract：BACKGROUND:Identification of the recombination hot/cold spots is critical for understanding the mechanism of recombination as well as the genome evolution process. However, experimental identification of recombination spots is both time-consuming and costly. Developing an accurate and automated method for reliably and ...

journal_title：BMC bioinformatics

authors： Li L,Yu S,Xiao W,Li Y,Huang L,Zheng X,Zhou S,Yang H

更新日期：2014-11-20 00:00:00

abstract：BACKGROUND:Protein-protein interactions play a key role in biological processes of proteins within a cell. Recent high-throughput techniques have generated protein-protein interaction data in a genome-scale. A wide range of computational approaches have been applied to interactome network analysis for uncovering functi...

journal_title：BMC bioinformatics

authors： Cho YR,Zhang A

更新日期：2010-04-29 00:00:00

abstract：BACKGROUND:Leishmania and other members of the Trypanosomatidae family diverged early on in eukaryotic evolution and consequently display unique cellular properties. Their apparent lack of transcriptional regulation is compensated by complex post-transcriptional control mechanisms, including the processing of polycistr...

journal_title：BMC bioinformatics

authors： Smith M,Blanchette M,Papadopoulou B

更新日期：2008-03-20 00:00:00

abstract：BACKGROUND:DNA methylation patterns store epigenetic information in the vast majority of eukaryotic species. The relatively high costs and technical challenges associated with the detection of DNA methylation however have created a bias in the number of methylation studies towards model organisms. Consequently, it rema...

journal_title：BMC bioinformatics

authors： Bulla I,Aliaga B,Lacal V,Bulla J,Grunau C,Chaparro C

更新日期：2018-03-27 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:People with an autistic spectrum disorder (ASD) display a variety of characteristic behavioral traits, including impaired social interaction, communication difficulties and repetitive behavior. This complex neurodevelopment disorder is known to be associated with a combination of genetic and environmental fa...

journal_title：BMC bioinformatics

authors： Patel S,Roncaglia P,Lovering RC

更新日期：2015-06-06 00:00:00

abstract：BACKGROUND:Barcode multiplexing is a key strategy for sharing the rising capacity of next-generation sequencing devices: Synthetic DNA tags, called barcodes, are attached to natural DNA fragments within the library preparation procedure. Different libraries, can individually be labeled with barcodes for a joint sequenc...

journal_title：BMC bioinformatics

authors： Kracht D,Schober S

更新日期：2015-02-18 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:Lineage rate heterogeneity can be a major source of bias, especially in multi-gene phylogeny inference. We had previously tackled this issue by developing LS3, a data subselection algorithm that, by removing fast-evolving sequences in a gene-specific manner, identifies subsets of sequences that evolve at a r...

journal_title：BMC bioinformatics

authors： Rivera-Rivera CJ,Montoya-Burgos JI

更新日期：2019-08-13 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:Analysis of sequence composition is a routine task in genome research. Organisms are characterized by their base composition, dinucleotide relative abundance, codon usage, and so on. Unique subsequences are markers of special interest in genome comparison, expression profiling, and genetic engineering. Relat...

journal_title：BMC bioinformatics

authors： Herold J,Kurtz S,Giegerich R

更新日期：2008-03-26 00:00:00

abstract：BACKGROUND:The development of high-throughput technologies has produced several large scale protein interaction data sets for multiple species, and significant efforts have been made to analyze the data sets in order to understand protein activities. Considering that the basic units of protein interactions are domain i...

journal_title：BMC bioinformatics

authors： Lee H,Deng M,Sun F,Chen T

更新日期：2006-05-25 00:00:00

abstract：BACKGROUND:Because loops connect regular secondary structures, analysis of the former depends directly on the definition of the latter. The numerous assignment methods, however, can offer different definitions. In a previous study, we defined a structural alphabet composed of 16 average protein fragments, which we call...

journal_title：BMC bioinformatics

authors： Fourrier L,Benros C,de Brevern AG

更新日期：2004-05-12 00:00:00

abstract：BACKGROUND:Our knowledge of global protein-protein interaction (PPI) networks in complex organisms such as humans is hindered by technical limitations of current methods. RESULTS:On the basis of short co-occurring polypeptide regions, we developed a tool called MP-PIPE capable of predicting a global human PPI network ...

journal_title：BMC bioinformatics

authors： Schoenrock A,Samanfar B,Pitre S,Hooshyar M,Jin K,Phillips CA,Wang H,Phanse S,Omidi K,Gui Y,Alamgir M,Wong A,Barrenäs F,Babu M,Benson M,Langston MA,Green JR,Dehne F,Golshani A

更新日期：2014-12-10 00:00:00

abstract：BACKGROUND:Simulated nucleotide or amino acid sequences are frequently used to assess the performance of phylogenetic reconstruction methods. BEAST, a Bayesian statistical framework that focuses on reconstructing time-calibrated molecular evolutionary processes, supports a wide array of evolutionary models, but lacked ...

journal_title：BMC bioinformatics

authors： Bielejec F,Lemey P,Carvalho LM,Baele G,Rambaut A,Suchard MA

更新日期：2014-05-07 00:00:00

abstract：BACKGROUND:Pattern matching is the core of bioinformatics; it is used in database searching, restriction enzyme mapping, and finding open reading frames. It is done repeatedly over increasingly long sequences, thus codes must be efficient and insensitive to sequence length. Such patterns of interest include simple moti...

journal_title：BMC bioinformatics

authors： Mangalam HJ

更新日期：2002-01-01 00:00:00

abstract：BACKGROUND:Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. There are many tools available for genome comparisons. Unfortunately, most of them are not applicable for the identification of unique genes and the inferen...

journal_title：BMC bioinformatics

authors： Lu G,Jiang L,Helikar RM,Rowley TW,Zhang L,Chen X,Moriyama EN

更新日期：2006-12-12 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:Maize is a leading crop in the modern agricultural industry that accounts for more than 40% grain production worldwide. THe double haploid technique that uses fewer breeding generations for generating a maize line has accelerated the pace of development of superior commercial seed varieties and has been tran...

journal_title：BMC bioinformatics

authors： Veeramani B,Raymond JW,Chanda P

更新日期：2018-08-13 00:00:00

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:Lung cancer is the leading cause of the largest number of deaths worldwide and lung adenocarcinoma is the most common form of lung cancer. In order to understand the molecular basis of lung adenocarcinoma, integrative analysis have been performed by using genomics, transcriptomics, epigenomics, proteomics an...

journal_title：BMC bioinformatics

authors： Zengin T,Önal-Süzek T

更新日期：2020-09-30 00:00:00

abstract：BACKGROUND:As molecular biology is creating an increasing amount of sequence and structure data, the multitude of software to analyze this data is also rising. Most of the programs are made for a specific task, hence the user often needs to combine multiple programs in order to reach a goal. This can make the data proc...

journal_title：BMC bioinformatics

authors： Kunzmann P,Hamacher K

更新日期：2018-10-01 00:00:00

abstract：BACKGROUND:Although high-throughput microarray based molecular diagnostic technologies show a great promise in cancer diagnosis, it is still far from a clinical application due to its low and instable sensitivities and specificities in cancer molecular pattern recognition. In fact, high-dimensional and heterogeneous tu...

journal_title：BMC bioinformatics

authors： Han H,Li XL

更新日期：2011-02-15 00:00:00

abstract：BACKGROUND:A fundamental fact in biology states that genes do not operate in isolation, and yet, methods that infer regulatory networks for single cell gene expression data have been slow to emerge. With single cell sequencing methods now becoming accessible, general network inference algorithms that were initially dev...

journal_title：BMC bioinformatics

authors： Chen S,Mar JC

更新日期：2018-06-19 00:00:00

abstract：BACKGROUND:Inflammation is a core element of many different, systemic and chronic diseases that usually involve an important autoimmune component. The clinical phase of inflammatory diseases is often the culmination of a long series of pathologic events that started years before. The systemic characteristics and relate...

journal_title：BMC bioinformatics

authors： Xiao H,Bartoszek K,Lio' P

更新日期：2018-11-30 00:00:00

abstract：BACKGROUND:Deep shotgun sequencing on next generation sequencing (NGS) platforms has contributed significant amounts of data to enrich our understanding of genomes, transcriptomes, amplified single-cell genomes, and metagenomes. However, deep coverage variations in short-read data sets and high sequencing error rates o...

journal_title：BMC bioinformatics

authors： McCorrison JM,Venepally P,Singh I,Fouts DE,Lasken RS,Methé BA

更新日期：2014-11-19 00:00:00

abstract：BACKGROUND:The sequencing of many genomes and tiling arrays consisting of millions of DNA segments spanning entire genomes have made high-resolution copy number analysis possible. Microarray-based comparative genomic hybridization (array CGH) has enabled the high-resolution detection of DNA copy number aberrations. Whi...

journal_title：BMC bioinformatics

authors： Skvortsov D,Abdueva D,Stitzer ME,Finkel SE,Tavaré S

更新日期：2007-06-14 00:00:00

abstract：BACKGROUND:Over one hundred different types of post-transcriptional RNA modifications have been identified in human. Researchers discovered that RNA modifications can regulate various biological processes, and RNA methylation, especially N6-methyladenosine, has become one of the most researched topics in epigenetics. ...

journal_title：BMC bioinformatics

authors： Wu X,Wei Z,Chen K,Zhang Q,Su J,Liu H,Zhang L,Meng J

更新日期：2019-05-02 00:00:00