jpHMM: Improving the reliability of recombination prediction in HIV-1 (2009)
Schultz, Anne-Kathrin, Zhang, Ming, Bulla, Ingo, Leitner, Thomas, Korber, Bette, Morgenstern, Burkhard, ...
Previously, we developed jumping profile hidden Markov model (jpHMM), a new method to detect recombinations in HIV-1 genomes. The jpHMM predicts recombination breakpoints in a query sequence and...
Keller, Oliver, Odronitz, Florian, Stanke, Mario, Kollmar, Martin, Waack, Stephan
Abstract Background For many types of analyses, data about gene structure and locations of non-coding regions of genes are required. Although a vast amount of genomic sequence data is available,...
A Jumping Profile HMM for Remote Protein Homology Detection (2008)
Anne-kathrin Schultz, Mario Stanke
We address the problem of finding new members of a given protein family in a database of protein sequences. Given a multiple sequence alignment (MSA) of the sequences in the protein family, we would...
The genome of the model beetle and pest Tribolium castaneum (2008)
Gibbs, Richard A, Weinstock, George M, Brown, Susan J, Denell, Robin, Beeman, Richard W, ...
Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural...
The genome of the model beetle and pest Tribolium castaneum (2008)
Gibbs, Richard A., Weinstock, George M., Brown, Susan J., Denell, Robin, Beeman, Richard W., ...
Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural...
Stanke, Mario, Tzvetkova, Ana, Morgenstern, Burkhard
Abstract Background A large number of gene prediction programs for the human genome exist. These annotation tools use a variety of methods and data sources. In the recent ENCODE genome annotation...
Schultz, Anne-Kathrin, Zhang, Ming, Leitner, Thomas, Kuiken, Carla, Korber, Bette, Morgenstern, Burkhard, ...
Abstract Background Jumping alignments have recently been proposed as a strategy to search a given multiple sequence alignment A against a database. Instead of comparing a database sequence S to the...
Stanke, Mario, Schöffmann, Oliver, Morgenstern, Burkhard, Waack, Stephan
Abstract Background In order to improve gene prediction, extrinsic evidence on the gene structure can be collected from various sources of information such as genome-genome comparisons and EST and...
Mario Stanke, Oliver Keller, Irfan Gunduz, Alec Hayes, Stephan Waack, Burkhard Morgenstern
AUGUSTUS is a software tool for gene prediction in eukaryotes based on a Generalized Hidden Markov Model, a probabilistic model of a sequence and its gene structure. Like most existing gene finders,...
AUGUSTUS: ab initio prediction of alternative transcripts (2006)
Stanke, Mario, Keller, Oliver, Gunduz, Irfan, Hayes, Alec, Waack, Stephan, Morgenstern, Burkhard
AUGUSTUS is a software tool for gene prediction in eukaryotes based on a Generalized Hidden Markov Model, a probabilistic model of a sequence and its gene structure. Like most existing gene finders,...
jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1 (2006)
Zhang, Ming, Schultz, Anne-Kathrin, Calef, Charles, Kuiken, Carla, Leitner, Thomas, Korber, Bette, ...
Detecting recombinations in the genome sequence of human immunodeficiency virus (HIV-1) is crucial for epidemiological studies and for vaccine development. Herein, we present a web server for...
Mario Stanke, Ana Tzvetkova, Burkhard Morgenstern
electronic version of this article is the complete one and can be
AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints (2005)
Stanke, Mario, Morgenstern, Burkhard
We present a WWW server for AUGUSTUS, a software for gene prediction in eukaryotic genomic sequences that is based on a generalized hidden Markov model, a probabilistic model of a sequence and its...
Sequential selection of random vectors under a sum constraint (2004)
We observe a sequence X1,X2,...,Xn of independent and identically distributed coordinatewise nonnegative d-dimensional random vectors. When a vector is observed it can either be selected or rejected...
Gene prediction with a hidden Markov model [Elektronische Ressource] / (2004)
Erscheinungsjahr an der Haupttitelstelle: 2003.
AUGUSTUS: a web server for gene finding in eukaryotes (2004)
Stanke, Mario, Steinkamp, Rasmus, Waack, Stephan, Morgenstern, Burkhard
We present a www server for AUGUSTUS, a novel software program for ab initio gene prediction in eukaryotic genomic sequences. Our method is based on a generalized Hidden Markov Model with a new...
Gene prediction with a Hidden Markov Model (2003)
Annotation of the large and rapidly increasing amount of genomic sequence data requires computational tools for finding genes in DNA sequences. This thesis presents a computational method for finding...
Gene prediction with a hidden Markov model and a new intron submodel (2003)
The problem of finding the genes in eukaryotic DNA sequences by computational methods is still not satisfactorily solved. Gene finding programs have achieved relatively high accuracy on short genomic...
Gene prediction with a hidden Markov model and a new intron submodel (2003)
Motivation: The problem of finding the genes in eukaryotic DNA sequences by computational methods is still not satisfactorily solved. Gene finding programs have achieved relatively high accuracy on...
AUGUSTUS: a web server for gene finding in eukaryotes
Stanke, Mario, Steinkamp, Rasmus, Waack, Stephan, Morgenstern, Burkhard
We present a www server for AUGUSTUS, a novel software program for ab initio gene prediction in eukaryotic genomic sequences. Our method is based on a generalized Hidden Markov Model with a new...
AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints
Stanke, Mario, Morgenstern, Burkhard
We present a WWW server for AUGUSTUS, a software for gene prediction in eukaryotic genomic sequences that is based on a generalized hidden Markov model, a probabilistic model of a sequence and its...
A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes
Schultz, Anne-Kathrin, Zhang, Ming, Leitner, Thomas, Kuiken, Carla, Korber, Bette, Morgenstern, Burkhard, ...
jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1
Zhang, Ming, Schultz, Anne-Kathrin, Calef, Charles, Kuiken, Carla, Leitner, Thomas, Korber, Bette, ...
Detecting recombinations in the genome sequence of human immunodeficiency virus (HIV-1) is crucial for epidemiological studies and for vaccine development. Herein, we present a web server for...
AUGUSTUS: ab initio prediction of alternative transcripts
Stanke, Mario, Keller, Oliver, Gunduz, Irfan, Hayes, Alec, Waack, Stephan, Morgenstern, Burkhard
AUGUSTUS is a software tool for gene prediction in eukaryotes based on a Generalized Hidden Markov Model, a probabilistic model of a sequence and its gene structure. Like most existing gene finders,...
AUGUSTUS: a web server for gene finding in eukaryotes
Stanke, Mario, Steinkamp, Rasmus, Waack, Stephan, Morgenstern, Burkhard
We present a www server for AUGUSTUS, a novel software program for ab initio gene prediction in eukaryotic genomic sequences. Our method is based on a generalized Hidden Markov Model with a new...
AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints
Stanke, Mario, Morgenstern, Burkhard
We present a WWW server for AUGUSTUS, a software for gene prediction in eukaryotic genomic sequences that is based on a generalized hidden Markov model, a probabilistic model of a sequence and its...
A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes
Schultz, Anne-Kathrin, Zhang, Ming, Leitner, Thomas, Kuiken, Carla, Korber, Bette, Morgenstern, Burkhard, ...
jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1
Zhang, Ming, Schultz, Anne-Kathrin, Calef, Charles, Kuiken, Carla, Leitner, Thomas, Korber, Bette, ...
Detecting recombinations in the genome sequence of human immunodeficiency virus (HIV-1) is crucial for epidemiological studies and for vaccine development. Herein, we present a web server for...
AUGUSTUS: ab initio prediction of alternative transcripts
Stanke, Mario, Keller, Oliver, Gunduz, Irfan, Hayes, Alec, Waack, Stephan, Morgenstern, Burkhard
AUGUSTUS is a software tool for gene prediction in eukaryotes based on a Generalized Hidden Markov Model, a probabilistic model of a sequence and its gene structure. Like most existing gene finders,...
Discovery and revision of Arabidopsis genes by proteogenomics
Castellana, Natalie E., Payne, Samuel H., Shen, Zhouxin, Stanke, Mario, Bafna, Vineet, Briggs, Steven P.
Gene annotation underpins genome science. Most often protein coding sequence is inferred from the genome based on transcript evidence and computational predictions. While generally correct, gene...
jpHMM: Improving the reliability of recombination prediction in HIV-1
Schultz, Anne-Kathrin, Zhang, Ming, Bulla, Ingo, Leitner, Thomas, Korber, Bette, Morgenstern, Burkhard, ...
Previously, we developed jumping profile hidden Markov model (jpHMM), a new method to detect recombinations in HIV-1 genomes. The jpHMM predicts recombination breakpoints in a query sequence and...