Refine
Has Fulltext
- yes (117)
Is part of the Bibliography
- yes (117)
Year of publication
Document Type
- Journal article (117) (remove)
Keywords
- metabolism (8)
- SARS-CoV-2 (5)
- apoptosis (5)
- cytokinins (5)
- COVID-19 (4)
- regulation (4)
- transcriptome (4)
- Candida albicans (3)
- bioinformatics (3)
- cisplatin (3)
- database (3)
- expression (3)
- identification (3)
- leukemic cells (3)
- molecular docking (3)
- mutation (3)
- systems biology (3)
- virulence (3)
- "-omics" (2)
- Aspergillus fumigatus (2)
- Bioinformatik (2)
- Biology (2)
- Caenorhabditis elegans (2)
- DNA (2)
- DNA storage (2)
- Metabolic pathways (2)
- RNA (2)
- Salmonella-containing vacuole (SCV) (2)
- adaptation (2)
- algorithm (2)
- alignment (2)
- annotation (2)
- cellular signalling networks (2)
- cytotoxicity (2)
- dendritic cells (2)
- differentiation (2)
- drug repurposing (2)
- engineering (2)
- evolution (2)
- infection (2)
- lung cancer (2)
- machine learning (2)
- metabolic modeling (2)
- molecular dynamics (2)
- mouse (2)
- oncolytic virus (2)
- oxidative stress (2)
- platelet (2)
- positive selection (2)
- recombination (2)
- resistance (2)
- synthetic biology (2)
- transcriptional regulation (2)
- 3D lung tumor tissue models (1)
- 3D tissue models (1)
- 6-benzylaminopurine (1)
- A2a-R receptor (1)
- ACKR4 (1)
- AIModules (1)
- AKT (1)
- Abstandsmessung (1)
- Aspergillus (1)
- Aspergillus fumigalus (1)
- Axl tyrosine kinase (1)
- B-cell (1)
- BRAF mutation (1)
- Berberine (1)
- Biologie (1)
- Boolean function (1)
- Boolean tree (1)
- C-60 fullerene (1)
- C60 fullerene (1)
- CD95 (1)
- CETCH cycle (1)
- CLAVATA3 (1)
- CLV3p (1)
- CO2-sequestration (1)
- C\(_{60}\) fullerene (1)
- Camponotus floridanus (1)
- Cell surface proteomics (1)
- Cestode (1)
- Chagas diagnosis (1)
- Chagas disease (1)
- Chagas monitoring (1)
- Chagas real time PCR (1)
- Chlamydia trachomatis (1)
- Computer modelling (1)
- Computer software (1)
- Cushing’s disease (1)
- DLS and AFM measurements (1)
- DNA damage (1)
- Doxorubicin (1)
- EMT (1)
- ERK signaling (1)
- Echinococcosis (1)
- Echinococcus (1)
- Einfluss (1)
- Embryonic induction (1)
- Enterobacteriaceae (1)
- Enzyme kinetics (1)
- Enzyme metabolism (1)
- Enzyme regulation (1)
- Enzymes (1)
- Epicardium-derived cells (1)
- Evaluation (1)
- FLS2 receptor (1)
- Functional modules (1)
- GPVI (1)
- Gene expression vectors (1)
- H7N9 influenza virus (1)
- HGPS (1)
- HIV (1)
- HeLa cells (1)
- Host-parasite interaction (1)
- Human atrial stromal cells (1)
- ICEP (1)
- ICP27 (1)
- IGFBP2 (1)
- Insulin (1)
- Integrated network analysis (1)
- IronChip Evaluation Package (1)
- KRAS biomarker signatures (1)
- Ki67 (1)
- Kinase inhibitor (1)
- Klimaneutralität (1)
- Klimapflanzen (1)
- Klimawandel (1)
- LS-MIDA (1)
- MHC I (1)
- MHC II (1)
- MITE (1)
- Metabolic profiles (1)
- Microarray (1)
- Mikroarray (1)
- Milnesium tardigradum (1)
- Mycoplasma (1)
- Neuromuscular junctions (1)
- Olea (1)
- Phylogenie (1)
- PknB (1)
- Polymerase chain reaction (1)
- Predictive toxicology (1)
- Prognose (1)
- Proteasen (1)
- Proteine (1)
- R0 (1)
- RNA secondary structure (1)
- RNA sequencing (1)
- RNA-SEQ (1)
- RNAi (1)
- Receptor kinase (1)
- Salmonella enterica (1)
- Salmonella-containing vacuole (1)
- Sanger sequencing (1)
- Septins (1)
- Shotgun method (1)
- Spumaviren (1)
- Staphylococcus aureus (1)
- Stp (1)
- Strukturanalyse (1)
- Synapses (1)
- Synaptic vesicles (1)
- Synthetic biology (1)
- T-cell (1)
- T-cell epitope (1)
- Tapeworm (1)
- Toxicity (1)
- Transcriptional control (1)
- Trend test (1)
- Trypanosoma (1)
- Trypanosoma cruzi (1)
- UV–Vis (1)
- V1–V9 (1)
- V4 (1)
- V7/V8 (1)
- VASP (1)
- Vasodilatator-stimuliertes Phosphoprotein (1)
- Vesicles (1)
- Virtual sequencing (1)
- WNT (1)
- Yolk protein (1)
- Zebrafish (1)
- Zika virus (1)
- abscisic acid (ABA) (1)
- accumulation (1)
- adaption (1)
- agent-based model (1)
- aging (1)
- alveolar fibrosis (1)
- alveolar regeneration (1)
- alzheimer's disease (1)
- alzheimers disease (1)
- animals (1)
- anti-cancer drug-like molecules (1)
- anti-thrombotic therapies (1)
- anticancer activity (1)
- antimicrobial peptides (1)
- antimycotics (1)
- antioxidants (1)
- antiproliferative (1)
- approved drugs (1)
- arabidopsis thaliana (1)
- arabidpsis thaliana (1)
- auxin (1)
- bacterial invasion (1)
- bacterial pathogens (1)
- bacteriology (1)
- beta-lactamase inhibition (1)
- binary decision diagram (1)
- binding pocket (1)
- binding protein (1)
- biofilm formation (1)
- biofuel (1)
- bioinformatics and computational biology (1)
- biological activities (1)
- biomanufacturing (1)
- biomarker (1)
- biomaterial surfaces (1)
- bioreactor culture (1)
- blood platelets (1)
- boolean in silico models (1)
- boolean modeling (1)
- brain (1)
- caenorhabditis elegans (1)
- calcium (1)
- calcium signaling pathway (1)
- camponotus floridanus (1)
- cancer therapy (1)
- candida genome database (1)
- carboxylation (1)
- carpenter ant (1)
- cascade (1)
- caspase-3 (1)
- cell death (1)
- cell staining (1)
- cell wall (1)
- centrality (1)
- cerebral ischemia (1)
- chemical similarity (1)
- chondrosarcoma (1)
- cluster (1)
- collagen (1)
- colony-stimulating factor (1)
- colorectal cancer (1)
- combinatorial drug predictions (1)
- comparative sequence analysis (1)
- complex networks (1)
- computational (1)
- computational biology and bioinformatics (1)
- computational modelling (1)
- computational prediction (1)
- computational systems biology (1)
- computer modelling (1)
- computer-assisted (1)
- connector (1)
- control group (1)
- control profiles (1)
- controllability (1)
- corticotropin-releasing hormone (1)
- crosstalk (1)
- cryptic (1)
- culture (1)
- cycle (1)
- cyclic nucleotide signaling (1)
- cytokinin (1)
- cytokinin kinetin (1)
- data mining/methods (1)
- data storage (1)
- defense and evasion strategies (1)
- defense signaling (1)
- defenses (1)
- design (1)
- deubiquitinases (1)
- differentially expressed genes (1)
- discovery (1)
- disease (1)
- docking (1)
- domain (1)
- doxorubicin (1)
- drosophila (1)
- drug design (1)
- drug release (1)
- drug resistance (1)
- drug-minded protein (1)
- dynamic protein-protein interactions (1)
- early diagnosis (1)
- efficient intervention points (1)
- elementary body (1)
- elementary modes (1)
- encapsulation (1)
- encephalitis dementia (1)
- enteric pathogens (1)
- enterica serovar Typhimurium (1)
- enzyme (1)
- epitope mapping (1)
- epitope prediction (1)
- error (1)
- error-transfer (1)
- eugenol (1)
- evolutionary (1)
- exome (1)
- explainability of machine learning (1)
- expressed sequence tag (1)
- facultatively intracellular pathogens (1)
- feature analysis (1)
- feature selection (1)
- flg22 (1)
- fluorescence recovery after photobleaching (1)
- flux balance analysis (1)
- format (1)
- fostamatinib (1)
- free energy (1)
- functional modules (1)
- fungal pathogens (1)
- fungicide (1)
- gamma (1)
- gene expression (1)
- gene ontology (1)
- genes (1)
- genetic regulatory network (1)
- genetic variation (1)
- genetics (1)
- genome browser (1)
- genus Aspergillus (1)
- guard cells (1)
- hepatotoxicity (1)
- histidine kinase (1)
- homology modeling (1)
- host-pathogen adaption (1)
- host-pathogen interaction (1)
- human (1)
- human immune system (1)
- human immunodeficiency virus (1)
- human pathogenic fungi (1)
- human xenografted mouse models (1)
- humans (1)
- image processing (1)
- imaging (1)
- immune system (1)
- immune-informatics (1)
- immunity (1)
- immunological cross-talk (1)
- immunotherapies (1)
- in silico simulation (1)
- in vitro (1)
- in vivo toxicity (1)
- in-vitro (1)
- infected-cell protein (1)
- infection biology (1)
- infection spread (1)
- inhibitor (1)
- interaction (1)
- interaction map (1)
- interaction networks (1)
- interactome (1)
- intermediate host (1)
- internal transcribed spacer 2 (1)
- interolog (1)
- interpolation (1)
- interspecies comparison (1)
- invasion (1)
- invasiveness (1)
- ion signaling (1)
- isotopolog profiling (1)
- kinase signaling (1)
- kinetin (1)
- lactate dehydrogenase (1)
- lethality rate (1)
- life-span regulation (1)
- light-gated proteins (1)
- lncRNAs (1)
- lymphocytes (1)
- lymphotoxicity (1)
- mammalian system (1)
- messenger RNA (1)
- meta-data (1)
- meta-transcriptome (1)
- metabolic flux (1)
- metabolic modelling (1)
- metabolic pathways (1)
- metabolomic profiling (1)
- miRNAs (1)
- microRNAs (1)
- microRNA–target interaction (1)
- microarray (1)
- microbes (1)
- model reduction (1)
- modeling (1)
- models (1)
- modular tumor tissue models (1)
- modulatory effects (1)
- molecular cloning (1)
- molecular dynamics simulation (1)
- molecular evolution (1)
- molecular modeling (1)
- molecular systematics (1)
- mortality (1)
- mosquito (1)
- mouse model (1)
- nanocarrier (1)
- nanocellulose (1)
- nanocomplex (1)
- natural language processing (1)
- natural processing (1)
- neisseria meningitidis (1)
- network (1)
- network analysis (1)
- network biology (1)
- network inference (1)
- network simulation (1)
- neuraminidase (1)
- next generation sequencing (1)
- nitric oxide (1)
- non-invasive biomarkers (1)
- noncovalent complex (1)
- noncovalent nanocomplex (1)
- nucleic acid motifs (1)
- olive (1)
- omics (1)
- optimal drug combination (1)
- optimal drug targeting (1)
- optimal pharmacological modulation (1)
- optimal treatment strategies (1)
- optogenetics (1)
- organogenesis (1)
- origin (1)
- pH (1)
- pangolin (1)
- parasite (1)
- pathogen-host interaction (PHI) (1)
- pathogenesis (1)
- pathogenicity (1)
- pathways (1)
- patient data (1)
- pharmacology (1)
- phosphoproteome (1)
- phosphorylation (1)
- photodynamic chemotherapy (1)
- photorespiration (1)
- phylogenetic analysis (1)
- phylogenetic tree (1)
- phylogenetics (1)
- phylogeny (1)
- phytohormones (1)
- plant hormones (1)
- plant system (1)
- pollen tube (1)
- population coverage (1)
- potential role (1)
- principal (1)
- pro-oxidant (1)
- progeria (1)
- promoter (1)
- protease; Indinavir; lead expansion; docking; pharmacophore (1)
- protein (1)
- protein analysis (1)
- protein chip (1)
- protein familiy (1)
- protein interaction database (1)
- protein-protein interaction (1)
- protein-protein interaction network (1)
- proteins (1)
- proteome (1)
- pseudomas-syringae (1)
- pyrazolo[3,4-d]pyrimidine (1)
- radiation (1)
- rational drug design (1)
- re-annotation (1)
- receptor (1)
- regulatory networks (1)
- relA (1)
- reliability (1)
- reproductive toxicity (1)
- response regulator (1)
- reticulate body (1)
- ribosomal RNA (1)
- riboswitch (1)
- richtersius coronifer (1)
- scaffold search (1)
- secondary structure (1)
- sensor (1)
- sequence (1)
- sequence alignment (1)
- shoot apical meristem (1)
- signaling (1)
- signaling network (1)
- signaling pathway (1)
- signalling (1)
- signalling pathways (1)
- silico model (1)
- simulation (1)
- single cell analysis (1)
- single-electron transistors (1)
- sky kinases (1)
- software (1)
- somatic mutations (1)
- spanlastic (1)
- splicing factors (1)
- stable state (1)
- stable-isotope (1)
- stem cell niche (1)
- stem-cell-triggered immunity (1)
- stemness (1)
- stratification (1)
- stringent response (1)
- structure (1)
- structure-activity relationship (1)
- sun exposure (1)
- superoxide-dismutase (1)
- synaptic vesicles (1)
- synergistic effect (1)
- synthetic pathways (1)
- system inference (1)
- tardigrada (1)
- target (1)
- targeted combination therapy (1)
- targeted therapy (1)
- targets (1)
- therapeutic strategy (1)
- thrombosis (1)
- tolerance (1)
- tools overview (1)
- transcription (1)
- translation (1)
- transmission (1)
- tumors (1)
- type 1 (1)
- uptake (1)
- variable regions (1)
- variants (1)
- virulenceregulatory evolution (1)
- viruses (1)
- vitellogenin (1)
- water stress (1)
- wrong labelling (1)
- xanthurenic acid (1)
- yvcK/glmR operon (1)
Institute
- Theodor-Boveri-Institut für Biowissenschaften (117) (remove)
Sonstige beteiligte Institutionen
EU-Project number / Contract (GA) number
- 031A408B (1)
- CoG 721016–HERPES (1)
- ESF-ZDEX 4.0 (1)
The ITS2 Database
(2012)
The internal transcribed spacer 2 (ITS2) has been used as a phylogenetic marker for more than two decades. As ITS2 research mainly focused on the very variable ITS2 sequence, it confined this marker to low-level phylogenetics only. However, the combination of the ITS2 sequence and its highly conserved secondary structure improves the phylogenetic resolution1 and allows phylogenetic inference at multiple taxonomic ranks, including species delimitation.
The ITS2 Database presents an exhaustive dataset of internal transcribed spacer 2 sequences from NCBI GenBank accurately reannotated. Following an annotation by profile Hidden Markov Models (HMMs), the secondary structure of each sequence is predicted. First, it is tested whether a minimum energy based fold (direct fold) results in a correct, four helix conformation. If this is not the case, the structure is predicted by homology modeling. In homology modeling, an already known secondary structure is transferred to another ITS2 sequence, whose secondary structure was not able to fold correctly in a direct fold.
The ITS2 Database is not only a database for storage and retrieval of ITS2 sequence-structures. It also provides several tools to process your own ITS2 sequences, including annotation, structural prediction, motif detection and BLAST search on the combined sequence-structure information. Moreover, it integrates trimmed versions of 4SALE and ProfDistS for multiple sequence-structure alignment calculation and Neighbor Joining tree reconstruction. Together they form a coherent analysis pipeline from an initial set of sequences to a phylogeny based on sequence and secondary structure.
In a nutshell, this workbench simplifies first phylogenetic analyses to only a few mouse-clicks, while additionally providing tools and data for comprehensive large-scale analyses.