BMC Bioinformatics
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srnaMapper: an optimal mapping tool for sRNA-Seq reads
BMC Bioinformatics - Tập 23 - Trang 1-19 - 2022
Sequencing is the key method to study the impact of short RNAs, which include micro RNAs, tRNA-derived RNAs, and piwi-interacting RNA, among others. The first step to make use of these reads is to map them to a genome. Existing mapping tools have been developed for long RNAs in mind, and, so far, no tool has been conceived for short RNAs. However, short RNAs have several distinctive features which......
A new protein-ligand binding sites prediction method based on the integration of protein sequence conservation information
BMC Bioinformatics - Tập 12 - Trang 1-7 - 2011
Prediction of protein-ligand binding sites is an important issue for protein function annotation and structure-based drug design. Nowadays, although many computational methods for ligand-binding prediction have been developed, there is still a demanding to improve the prediction accuracy and efficiency. In addition, most of these methods are purely geometry-based, if the prediction methods improve......
Practical application of a Bayesian network approach to poultry epigenetics and stress
BMC Bioinformatics - Tập 23 - Trang 1-16 - 2022
Relationships among genetic or epigenetic features can be explored by learning probabilistic networks and unravelling the dependencies among a set of given genetic/epigenetic features. Bayesian networks (BNs) consist of nodes that represent the variables and arcs that represent the probabilistic relationships between the variables. However, practical guidance on how to make choices among the wide ......
RRCRank: a fusion method using rank strategy for residue-residue contact prediction
BMC Bioinformatics - Tập 18 - Trang 1-12 - 2017
In structural biology area, protein residue-residue contacts play a crucial role in protein structure prediction. Some researchers have found that the predicted residue-residue contacts could effectively constrain the conformational search space, which is significant for de novo protein structure prediction. In the last few decades, related researchers have developed various methods to predict res......
libgapmis: extending short-read alignments
BMC Bioinformatics - Tập 14 - Trang 1-14 - 2013
A wide variety of short-read alignment programmes have been published recently to tackle the problem of mapping millions of short reads to a reference genome, focusing on different aspects of the procedure such as time and memory efficiency, sensitivity, and accuracy. These tools allow for a small number of mismatches in the alignment; however, their ability to allow for gaps varies greatly, with ......
Identifying microRNA targets in different gene regions
BMC Bioinformatics - Tập 15 - Trang 1-11 - 2014
Currently available microRNA (miRNA) target prediction algorithms require the presence of a conserved seed match to the 5' end of the miRNA and limit the target sites to the 3' untranslated regions of mRNAs. However, it has been noted that these requirements may be too stringent, leading to a substantial number of missing targets. We have developed TargetS, a novel computational approach for predi......
Automatic plankton image classification combining multiple view features via multiple kernel learning
BMC Bioinformatics - Tập 18 - Trang 1-18 - 2017
Plankton, including phytoplankton and zooplankton, are the main source of food for organisms in the ocean and form the base of marine food chain. As the fundamental components of marine ecosystems, plankton is very sensitive to environment changes, and the study of plankton abundance and distribution is crucial, in order to understand environment changes and protect marine ecosystems. This study w......
Fold change rank ordering statistics: a new method for detecting differentially expressed genes
BMC Bioinformatics - Tập 15 - Trang 1-15 - 2014
Different methods have been proposed for analyzing differentially expressed (DE) genes in microarray data. Methods based on statistical tests that incorporate expression level variability are used more commonly than those based on fold change (FC). However, FC based results are more reproducible and biologically relevant. We propose a new method based on fold change rank ordering statistics (FCROS......
Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis
BMC Bioinformatics - Tập 11 - Trang 1-11 - 2010
Analysis of data from high-throughput experiments depends on the availability of well-structured data that describe the assayed biomolecules. Procedures for obtaining and organizing such meta-data on genes, transcripts and proteins have been streamlined in many data analysis packages, but are still lacking for metabolites. Chemical identifiers are notoriously incoherent, encompassing a wide range ......
Are orphan genes protein-coding, prediction artifacts, or non-coding RNAs?
BMC Bioinformatics - Tập 17 - Trang 1-13 - 2016
Current genome sequencing projects reveal substantial numbers of taxonomically restricted, so called orphan genes that lack homology with genes from other evolutionary lineages. However, it is not clear to what extent orphan genes are real, genomic artifacts, or represent non-coding RNAs. Here, we use a simple set of assumptions to test the nature of orphan genes. First, a sequence that is transcr......
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