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mGene: Accurate Computational Gene Finding — Raetsch-Lab

mGene is a computational tool for the genome-wide prediction of protein coding genes from eukaryotic DNA sequences. It is based on recent advances in machine learning and uses discriminative training techniques, such as support vector machines (SVMs) and hidden semi-Markov support vector machines (HSMSVMs). Its excellent performance was proved in an objective competition based on the genome of the nematode Caenorhabditis elegans. The evaluated developmental version of mGene exhibited the best prediction per

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mGene: Accurate Computational Gene Finding — Raetsch-Lab | mgene.org Reviews

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mGene is a computational tool for the genome-wide prediction of protein coding genes from eukaryotic DNA sequences. It is based on recent advances in machine learning and uses discriminative training techniques, such as support vector machines (SVMs) and hidden semi-Markov support vector machines (HSMSVMs). Its excellent performance was proved in an objective competition based on the genome of the nematode Caenorhabditis elegans. The evaluated developmental version of mGene exhibited the best prediction per

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cbio@mskcc,directory,research,bioinformatics core,publications,tools,opportunities,contact cbio,education,personal tools,rarr;,rätsch lab,supplements,info,news,paper describing,mgene,mgeneweb,software release,mgene 0 1 0 beta,download mgene,nucleotide

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mGene: Accurate Computational Gene Finding — Raetsch-Lab | mgene.org Reviews

https://mgene.org

mGene is a computational tool for the genome-wide prediction of protein coding genes from eukaryotic DNA sequences. It is based on recent advances in machine learning and uses discriminative training techniques, such as support vector machines (SVMs) and hidden semi-Markov support vector machines (HSMSVMs). Its excellent performance was proved in an objective competition based on the genome of the nematode Caenorhabditis elegans. The evaluated developmental version of mGene exhibited the best prediction per

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mgene.org

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Genome Predictions — Raetsch-Lab

http://www.mgene.org/predictions

Memorial Sloan-Kettering Cancer Center. MGene: A Novel Discriminative Gene Finding System. MGene C brenneri PB2801-4.0.gff3.bz2. MGene C briggsae WS180 cb3.gff3.bz2. MGene C elegans WS180.gff3.bz2. MGene C remanei wustl-15.0.1.gff3.bz2. MGene C japonica draft assemply 3.0.2.gff3.bz2. MGene B malayi brugia WS185.gff3.bz2.

2

mGene.web: A Web Service for Accurate Computational Gene Finding — Raetsch-Lab

http://www.mgene.org/web

Memorial Sloan-Kettering Cancer Center. MGene: A Novel Discriminative Gene Finding System. MGeneweb: A Web Service for Accurate Computational Gene Finding. The web service has been described in [1]. And can be found here: http:/ galaxy.raetschlab.org. Is an interface to the. Gene finding system (see http:/ mgene.org. For more details) that is available for download at http:/ mgene.org/download. Simple one-step procedure to. Gene predictor for a new organism based on a FASTA and a GFF3 (or GTF) file.

3

mGene.web Performance — Raetsch-Lab

http://www.mgene.org/web/performance

Memorial Sloan-Kettering Cancer Center. MGene: A Novel Discriminative Gene Finding System. Performance of Signal Predictors for Various Species. Performance of Content Predictors for Various Species. Performance of Gene Prediction for various Species. Gene set all genes have been used for training and testing (i.e. there was no independent test set). These are preliminary results generated with a beta version of.

4

Methods — Raetsch-Lab

http://www.mgene.org/methods

Memorial Sloan-Kettering Cancer Center. MGene: A Novel Discriminative Gene Finding System. That operates directly on DNA sequences as input, some use additional Spectrum kernels [3]. In the second step, the outputs of all layer 1 sensors are combined in order to predict gene structures (segmentations). To this end, we extended the hidden semi-Markov SVM framework [1]. Gunnar Rätsch and Sören Sonnenburg. Large Scale Hidden Semi-Markov SVMs. In Advances in Neural Information Processing Systems 19, ...Sören...

5

mGene: Accurate Computational Gene Finding — Raetsch-Lab

http://www.mgene.org/suppl

Memorial Sloan-Kettering Cancer Center. MGene: A Novel Discriminative Gene Finding System. MGene: Accurate Computational Gene Finding. July 9, 2010. Talk on Next Generation Genome Annotation with mGene.ngs. At ISCB Student Council Symposium. June 23, 2009. Accepted for publication in Genome Research [3]. June 3, 2009. Published in Nucleic Acids Research [1]. June 1, 2009. Is available for download at http:/ mgene.org/download. March 1, 2009. MGeneweb goes live, see http:/ mgene.org/web. Compared to state...

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mGene: Accurate Computational Gene Finding — Raetsch-Lab

Memorial Sloan-Kettering Cancer Center. MGene: A Novel Discriminative Gene Finding System. MGene: Accurate Computational Gene Finding. July 9, 2010. Talk on Next Generation Genome Annotation with mGene.ngs. At ISCB Student Council Symposium. June 23, 2009. Accepted for publication in Genome Research [3]. June 3, 2009. Published in Nucleic Acids Research [1]. June 1, 2009. Is available for download at http:/ mgene.org/download. March 1, 2009. MGeneweb goes live, see http:/ mgene.org/web. Compared to state...

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