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This Web Service accesses the database records and various tools of the GenomeAtlas database v3. The records maintained by this database are synchronized regularly with the Entrez Genome Project (http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi?view=1) # # DATABASE LOOK-UP FUNCTIONS # 1. getSeq Get one or more genomic sequences from the Genome Atlas database (update regularly against Entrez Microbial Genomes), providing the genbank accession number. Input: …
Provider: Center for Biological Sequence Analysis (CBS)
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SIDDbase-WS is a SOAP based Web Service created in a collaboration between the Comparative Microbial Genomics Group at CBS, The Technical University of Denmark and Prof. Craig Benham’s research group at the UC Davis Genome Center. It provides interoperable access to the SIDD software, and access to the repository of stored results from calculations previously performed on complete bacterial genomes. SIDD (Stress-induced DNA Duplex Destabilization) is the propensity for the DNA …
Provider: Center for Biological Sequence Analysis (CBS)
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INTRODUCTION This Web Service implements NetGlycate 1.0. It predicts glycation of Epsilon amino groups of lysines in mammalian proteins. The method is described in detail in the following article: Analysis and prediction of mammalian protein glycation. Morten Bo Johansen, Lars Kiemer and Soren Brunak Glycobiology, 16:844-853, 2006. Alongside this Web Service the NetGlycate method is also implemented as a traditional paste-and-click WWW server at: http://…
Provider: Center for Biological Sequence Analysis (CBS)
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INTRODUCTION This Web Service implements NetNGlyc 1.0b. It predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons. The method is described in detail in the following article: “Prediction of N-glycosylation sites in human proteins”. R. Gupta, E. Jung and S. Brunak. In preparation, 2004. Alongside this Web Service the NetNGlyc method is also implemented as a traditional int…
Provider: Center for Biological Sequence Analysis (CBS)
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INTRODUCTION This Web Service implements NetOGlyc 3.1d. It predicts mucin type GalNAc O-glycosylation sites in mammalian proteins. The method is described in detail in the following article: “Prediction, conservation analysis and structural characterization of mammalian mucin-type O-glycosylation sites”. K. Julenius, A. Moelgaard, R. Gupta and S. Brunak. Glycobiology, 15:153-164, 2005. Alongside this Web Service the NetOGlyc method is also implemented as a tr…
Provider: Center for Biological Sequence Analysis (CBS)
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INTRODUCTION This Web Service implements hERG 1.0. It predicts cardiotoxicity of drug molecules. The method is described in detail in the following article: hERG Classification Model Based on a Combination of Support Vector Machine Method and GRIND Descriptors. Li Q, Joergensen FS, Oprea T, Brunak S, Taboureau O. Mol Pharm: 4;5:117-127, 2008. Alongside this Web Service the hERG method is also implemented as a traditional paste-and-click WWW server at: ht…
Provider: Center for Biological Sequence Analysis (CBS)
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This service provides an external access to the GeneWiz software developed at CBS (Pedersen AG et al. 2000) The program visualizes DNA parameters and annotations in either a circular or linear representation. 1. runGenewiz The atlas can display two conceptually different kinds of information: Annotations and data. Annotations are plotted with a fixed color in the entire range in which it is defined. Annotations are divided into features (e.g. CDS, rRNA, tRNA et…
Provider: Center for Biological Sequence Analysis (CBS)
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INTRODUCTION This Web Service implements SignalP v. 3.1. It predictsthe presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks and hidden Markov models. The method is described in detail in t…
Provider: Center for Biological Sequence Analysis (CBS)
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INTRODUCTION This Web Service implements SignalP v. 3.0. It predictsthe presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks and hidden Markov models. The method is described in detail in the fol…
Provider: Center for Biological Sequence Analysis (CBS)
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INTRODUCTION This Web Service implements NetCTL v. 1.1. It predicts CTL epitopes in protein sequences integrating prediction of peptide MHC binding, proteasomal C terminal cleavage and TAP transport efficiency. The method is described in detail in the following article: An integrative approach to CTL epitope prediction. A combined algorithm integrating MHC-I binding, TAP transport efficiency, and proteasomal cleavage predictions. Larsen MV, Lundegaard C, Kasper Lambert…
Provider: Center for Biological Sequence Analysis (CBS)
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This Web Service predicts location of ribosomal RNA genes in full genome sequences by using Hidden Markov Models based on alignments from a highly cureated dataset of structurally aligned sequnces. The input is one or more genomic sequence(s) as either one or more contigs. Each contig is submitted as one continous string of DNA together with the sequences identifier. The kingdom (either Bacteria, Archaea, or Eukaryotes) is specified once for each job that is submitted, using th…
Provider: Center for Biological Sequence Analysis (CBS)
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The EasyGene 1.0 server produces a list of predicted genes given a sequence of prokaryotic DNA. Each prediction is attributed with a significance score (R-value) indicating how likely it is to be just a non-coding open reading frame rather than a real gene. The user needs only to specify the organism hosting the query sequence. Two more parameters (start codon leniency and R-value cutoff) have default values which may be altered if needed. http://www.cbs.dtu.dk/services/EasyGene…
Provider: Center for Biological Sequence Analysis (CBS)
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The EasyGene 1.0 server produces a list of predicted genes given a sequence of prokaryotic DNA. Each prediction is attributed with a significance score (R-value) indicating how likely it is to be just a non-coding open reading frame rather than a real gene. The user needs only to specify the organism hosting the query sequence. Two more parameters (start codon leniency and R-value cutoff) have default values which may be altered if needed. http://www.cbs.dtu.dk/services/EasyGene…
Provider: Center for Biological Sequence Analysis (CBS)
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INTRODUCTION This Web Service implements NetPhos 3.1b. It predicts serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins using ensembles of neural networks. Both generic and kinase specific predictions are performed. The method is described in detail in the following articles. Generic predictions: “Sequence and structure-based prediction of eukaryotic protein phosphorylation sites”. Blom N, Gammeltoft S, Brunak S (1999). J Mol Biol. 199…
Provider: Center for Biological Sequence Analysis (CBS)
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TMHMM is a method for prediction transmembrane helices based on a hidden Markov model and developed by Anders Krogh and Erik Sonnhammer. The method is described in detail in the following articles: Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. A. Krogh, B. Larsson, G. von Heijne, and E. L. L. Sonnhammer. J. Mol. Biol., 305(3):567-580, January 2001. PDF: http://www.binf.ku.dk/krogh/publications/pdf/KroghEtal01…
Provider: Center for Biological Sequence Analysis (CBS)
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INTRODUCTION This Web Service implements NetChop v. 3.1. It produces neural network predictions for cleavage sites of the human proteasome. The method is described in detail in the following article: The role of the proteasome in generating cytotoxic T cell epitopes: Insights obtained from improved predictions of proteasomal cleavage. M Nielsen, C Lundegaard, O Lund, and C Kesmir. Immunogenetics., 57(1-2):33-41, 2005. Alongside this Web Service the NetChop method is als…
Provider: Center for Biological Sequence Analysis (CBS)
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The EasyGene 1.0 server produces a list of predicted genes given a sequence of prokaryotic DNA. Each prediction is attributed with a significance score (R-value) indicating how likely it is to be just a non-coding open reading frame rather than a real gene. The user needs only to specify the organism hosting the query sequence. Two more parameters (start codon leniency and R-value cutoff) have default values which may be altered if needed. http://www.cbs.dtu.dk/services/EasyGene…
Provider: Center for Biological Sequence Analysis (CBS)
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SIDDbase-WS is a SOAP based Web Service created in a collaboration between the Comparative Microbial Genomics Group at CBS, The Technical University of Denmark and Prof. Craig Benham’s research group at the UC Davis Genome Center. It provides interoperable access to the SIDD software, and access to the repository of stored results from calculations previously performed on complete bacterial genomes. SIDD (Stress-induced DNA Duplex Destabilization) is the propensity for the DNA…