Abstract:
BACKGROUND:Analyses of biomolecules for biodiversity, phylogeny or structure/function studies often use graphical tree representations. Many powerful tree editors are now available, but existing tree visualization tools make little use of meta-information related to the entities under study such as taxonomic descriptions or gene functions that can hardly be encoded within the tree itself (if using popular tree formats). Consequently, a tedious manual analysis and post-processing of the tree graphics are required if one needs to use external information for displaying or investigating trees. RESULTS:We have developed TreeDyn, a tool using annotations and dynamic graphical methods for editing and analyzing multiple trees. The main features of TreeDyn are 1) the management of multiple windows and multiple trees per window, 2) the export of graphics to several standard file formats with or without HTML encapsulation and a new format called TGF, which enables saving and restoring graphical analysis, 3) the projection of texts or symbols facing leaf labels or linked to nodes, through manual pasting or by using annotation files, 4) the highlight of graphical elements after querying leaf labels (or annotations) or by selection of graphical elements and information extraction, 5) the highlight of targeted trees according to a source tree browsed by the user, 6) powerful scripts for automating repetitive graphical tasks, 7) a command line interpreter enabling the use of TreeDyn through CGI scripts for online building of trees, 8) the inclusion of a library of packages dedicated to specific research fields involving trees. CONCLUSION:TreeDyn is a tree visualization and annotation tool which includes tools for tree manipulation and annotation and uses meta-information through dynamic graphical operators or scripting to help analyses and annotations of single trees or tree collections.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Chevenet F,Brun C,Bañuls AL,Jacq B,Christen Rdoi
10.1186/1471-2105-7-439subject
Has Abstractpub_date
2006-10-10 00:00:00pages
439issn
1471-2105pii
1471-2105-7-439journal_volume
7pub_type
杂志文章abstract:BACKGROUND:The main research topic in this paper is how to compare multiple biological experiments using transcriptome data, where each experiment is measured and designed to compare control and treated samples. Comparison of multiple biological experiments is usually performed in terms of the number of DEGs in an arbi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3302-7
更新日期:2019-12-27 00:00:00
abstract:BACKGROUND:Non-negative matrix factorisation (NMF), a machine learning algorithm, has been applied to the analysis of microarray data. A key feature of NMF is the ability to identify patterns that together explain the data as a linear combination of expression signatures. Microarray data generally includes individual e...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-175
更新日期:2006-03-28 00:00:00
abstract:BACKGROUND:Improvements in technology have been accompanied by the generation of large amounts of complex data. This same technology must be harnessed effectively if the knowledge stored within the data is to be retrieved. Storing data in ontologies aids its management; ontologies serve as controlled vocabularies that ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-74
更新日期:2005-03-24 00:00:00
abstract:BACKGROUND:Pseudouridylation is the most prevalent type of posttranscriptional modification in various stable RNAs of all organisms, which significantly affects many cellular processes that are regulated by RNA. Thus, accurate identification of pseudouridine (Ψ) sites in RNA will be of great benefit for understanding t...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2321-0
更新日期:2018-08-29 00:00:00
abstract:BACKGROUND:Integrative network methods are commonly used for interpretation of high-throughput experimental biological data: transcriptomics, proteomics, metabolomics and others. One of the common approaches is finding a connected subnetwork of a global interaction network that best encompasses significant individual c...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03572-9
更新日期:2020-11-18 00:00:00
abstract:BACKGROUND:We introduce Approximate Entropy as a mathematical method of analysis for microarray data. Approximate entropy is applied here as a method to classify the complex gene expression patterns resultant of a clinical sample set. Since Entropy is a measure of disorder in a system, we believe that by choosing genes...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-66
更新日期:2009-02-20 00:00:00
abstract:BACKGROUND:Chemical named entities represent an important facet of biomedical text. RESULTS:We have developed a system to use character-based n-grams, Maximum Entropy Markov Models and rescoring to recognise chemical names and other such entities, and to make confidence estimates for the extracted entities. An adjusta...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-S11-S4
更新日期:2008-11-19 00:00:00
abstract:BACKGROUND:Ontology term labels can be ambiguous and have multiple senses. While this is no problem for human annotators, it is a challenge to automated methods, which identify ontology terms in text. Classical approaches to word sense disambiguation use co-occurring words or terms. However, most treat ontologies as si...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-28
更新日期:2009-01-21 00:00:00
abstract:BACKGROUND:Computational discovery of microRNAs (miRNA) is based on pre-determined sets of features from miRNA precursors (pre-miRNA). Some feature sets are composed of sequence-structure patterns commonly found in pre-miRNAs, while others are a combination of more sophisticated RNA features. In this work, we analyze t...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-124
更新日期:2014-05-02 00:00:00
abstract:BACKGROUND:Protein quality assessment (QA) useful for ranking and selecting protein models has long been viewed as one of the major challenges for protein tertiary structure prediction. Especially, estimating the quality of a single protein model, which is important for selecting a few good models out of a large model ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1405-y
更新日期:2016-12-05 00:00:00
abstract:BACKGROUND:Protein function prediction is an important problem in the post-genomic era. Recent advances in experimental biology have enabled the production of vast amounts of protein-protein interaction (PPI) data. Thus, using PPI data to functionally annotate proteins has been extensively studied. However, most existi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-S12-S4
更新日期:2013-01-01 00:00:00
abstract:BACKGROUND:Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain datab...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-4-16
更新日期:2003-05-06 00:00:00
abstract:BACKGROUND:Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to the reference genome. Recently it became possible to reconcile both of these types of large-scale va...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3208-4
更新日期:2019-12-17 00:00:00
abstract:BACKGROUND:Large-scale genomic studies based on transcriptome technologies provide clusters of genes that need to be functionally annotated. The Gene Ontology (GO) implements a controlled vocabulary organised into three hierarchies: cellular components, molecular functions and biological processes. This terminology all...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-241
更新日期:2006-05-04 00:00:00
abstract:BACKGROUND:Protein-protein interactions (PPIs) are of great importance in cellular systems of organisms, since they are the basis of cellular structure and function and many essential cellular processes are related to that. Most proteins perform their functions by interacting with other proteins, so predicting PPIs acc...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03896-6
更新日期:2020-12-16 00:00:00
abstract:BACKGROUND:Identifying the interactions between proteins and long non-coding RNAs (lncRNAs) is of great importance to decipher the functional mechanisms of lncRNAs. However, current experimental techniques for detection of lncRNA-protein interactions are limited and inefficient. Many methods have been proposed to predi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2390-0
更新日期:2018-10-11 00:00:00
abstract:BACKGROUND:Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic seq...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-227
更新日期:2014-06-30 00:00:00
abstract:BACKGROUND:The efficient and robust statistical analysis of the shape of plant organs of different cultivars is an important investigation issue in plant breeding and enables a robust cultivar description within the breeding progress. Laserscanning is a highly accurate and high resolution technique to acquire the 3D sh...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03654-8
更新日期:2020-07-29 00:00:00
abstract:BACKGROUND:Protein-protein interactions (PPIs) are central to many biological processes. Considering that the experimental methods for identifying PPIs are time-consuming and expensive, it is important to develop automated computational methods to better predict PPIs. Various machine learning methods have been proposed...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03646-8
更新日期:2020-07-21 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
pub_type: 杂志文章
doi:10.1186/1471-2105-11-S2-S2
更新日期:2010-04-16 00:00:00
abstract:BACKGROUND:It has long been recognized that sensitivity analysis plays a key role in modeling and analyzing cellular and biochemical processes. Systems biology markup language (SBML) has become a well-known platform for coding and sharing mathematical models of such processes. However, current SBML compatible software ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-342
更新日期:2008-08-15 00:00:00
abstract:BACKGROUND:In the past decade, bioinformatics tools have matured enough to reliably perform sophisticated primary data analysis on Next Generation Sequencing (NGS) data, such as mapping, assemblies and variant calling, however, there is still a dire need for improvements in the higher level analysis such as NGS data or...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-167
更新日期:2013-05-28 00:00:00
abstract:BACKGROUND:Bioinformatics tools for automatic processing of biomedical literature are invaluable for both the design and interpretation of large-scale experiments. Many information extraction (IE) systems that incorporate natural language processing (NLP) techniques have thus been developed for use in the biomedical fi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-325
更新日期:2007-09-01 00:00:00
abstract:BACKGROUND:Ontologies are widely used to represent knowledge in biomedicine. Systematic approaches for detecting errors and disagreements are needed for large ontologies with hundreds or thousands of terms and semantic relationships. A recent approach of defining terms using logical definitions is now increasingly bein...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-418
更新日期:2011-10-27 00:00:00
abstract:BACKGROUND:Biocatalysis in organic solvents is nowadays a common practice with a large potential in Biotechnology. Several studies report that proteins which are co-crystallized or soaked in organic solvents preserve their fold integrity showing almost identical arrangements when compared to their aqueous forms. Howeve...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2044-2
更新日期:2018-01-30 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
pub_type: 杂志文章
doi:10.1186/1471-2105-7-S5-S16
更新日期:2006-12-18 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
pub_type: 杂志文章
doi:10.1186/s12859-016-1237-9
更新日期:2016-09-17 00:00:00
abstract:BACKGROUND:During the past decade, many software packages have been developed for analysis and visualization of various types of microarrays. We have developed and maintained the widely used dChip as a microarray analysis software package accessible to both biologist and data analysts. However, challenges arise when dC...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-231
更新日期:2008-05-08 00:00:00
abstract:BACKGROUND:T-cells are key players in regulating a specific immune response. Activation of cytotoxic T-cells requires recognition of specific peptides bound to Major Histocompatibility Complex (MHC) class I molecules. MHC-peptide complexes are potential tools for diagnosis and treatment of pathogens and cancer, as well...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-3-25
更新日期:2002-09-11 00:00:00
abstract:BACKGROUND:The molecular recognition based on the complementary base pairing of deoxyribonucleic acid (DNA) is the fundamental principle in the fields of genetics, DNA nanotechnology and DNA computing. We present an exhaustive DNA sequence design algorithm that allows to generate sets containing a maximum number of seq...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-138
更新日期:2012-06-20 00:00:00