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Orphelia - Metagenomic ORf FINder

Orphelia predicts genes in DNA fragments from species that were not included in the training set with good accuracy, and in particular, with a high specificity. 1] K J. Hoff, M. Tech, T. Lingner, R. Daniel, B. Morgenstern, P. Meinicke (2008) Gene prediction in metagenomic fragments: a large scale machine learning approach. 2] K J. Hoff, T. Lingner, P. Meinicke, M. Tech (2009) Orphelia: predicting genes in metagenomic sequencing reads Nucleic Acids Research.

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Orphelia - Metagenomic ORf FINder | orphelia.gobics.de Reviews

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Orphelia predicts genes in DNA fragments from species that were not included in the training set with good accuracy, and in particular, with a high specificity. 1] K J. Hoff, M. Tech, T. Lingner, R. Daniel, B. Morgenstern, P. Meinicke (2008) Gene prediction in metagenomic fragments: a large scale machine learning approach. 2] K J. Hoff, T. Lingner, P. Meinicke, M. Tech (2009) Orphelia: predicting genes in metagenomic sequencing reads Nucleic Acids Research.

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Orphelia - Metagenomic ORf FINder | orphelia.gobics.de Reviews

https://orphelia.gobics.de

Orphelia predicts genes in DNA fragments from species that were not included in the training set with good accuracy, and in particular, with a high specificity. 1] K J. Hoff, M. Tech, T. Lingner, R. Daniel, B. Morgenstern, P. Meinicke (2008) Gene prediction in metagenomic fragments: a large scale machine learning approach. 2] K J. Hoff, T. Lingner, P. Meinicke, M. Tech (2009) Orphelia: predicting genes in metagenomic sequencing reads Nucleic Acids Research.

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orphelia.gobics.de

1

Orphelia - Gene finding in fragments

http://orphelia.gobics.de/datasets.jsp

We provide the training data in Matlab. Vector format (*.mat). The neural net is based on Netlab. Structs. For evaluation the test fragments are provided as plain sequence files (*.seq) with the corresponding predictions by our method (*.coords) and genomic coordinates of the fragment (*.cuts). Detailed description of the data and the model. Matlab-file, 59 k). Matlab-file, 255 MB). Matlab-file, 155 MB). Matlab-file, 489 MB). Tgz, 1.2 GB, decompressed 5.6 GB).

2

Orphelia - Metagenomic ORF Finder

http://orphelia.gobics.de/results.jsp

The performance of Orphelia with the models Net300 and Net700 was evaluated on randomly excised DNA fragments of 300 bp and 700 bp length. The fragments were sampled to 10-fold genome coverage from the species Archeaoglobus fulgidus, Methanococcus jannaschii, Natronomonas pharaonis, Buchnera aphidicola, Bacillus subtilis, Corynebacterium jeikeium, Chlorobium tepidum, Escherichia coli, Helicobacter pylori, Prochlorococcus marinus, and Wolbachia endosymbiont. Mean and standard deviation were calcul...3] No...

3

Orphelia Submission

http://orphelia.gobics.de/submission

What is the model? Nt What is the »Max overlap«? Paste your sequences in multiple FASTA format. For datasets up to 30 MB:. Upload your sequences file in multiple FASTA format. If your data exceedes the maximum for upload, you can download. The stand alone tool and run Orphelia locally. This website is free and open to all users and there is no login requirement. Please direct your questions and comments to orphelia-info@gobics.de.

4

Orphelia - Metagenomic ORF Finder

http://orphelia.gobics.de/help.jsp

Orphelia currently provides two models for scoring open reading frames in sequence fragments, Net700 and Net300. In order to run the webserver, you need to specify, which model should be used to predict genes in your input data. Net700 was trained on 700 bp fragments. This model should be used for input data of Sanger read length ( 700 bp) or longer. Below sensitivity and specificity for both models in the range of 200 to 500 bp is provided. Click on the figures to get a fullscreen view. Seq No 1 CCTCCTC...

5

Orphelia - Metagenomic ORf FINder

http://orphelia.gobics.de/download.jsp

Download the command line tool Orphelia for Linux, 64 bit architecture. Tgz, 68 MB). Please direct your questions and comments to orphelia-info@gobics.de.

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gobics.de: Software

http://gobics.de/department/software

University of Göttingen. Faculty of Biology and Psychology. Institute of Microbiology and Genetics. Software tools available through GOBICS (GÃ ttingen Bioinformatics Compute Server):. Alignment free sequence comparison. A web-server for fast comparative functional profiling of metagenomes. Gene prediction for eukaryotes. Ultra-fast functional profiling of large protein sequence collections. Clustering and Visualization of Metabolic Markers. Multiple sequence alignment; various program versions available.

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orphelia.gobics.de

Orphelia - Metagenomic ORf FINder

Orphelia predicts genes in DNA fragments from species that were not included in the training set with good accuracy, and in particular, with a high specificity. 1] K J. Hoff, M. Tech, T. Lingner, R. Daniel, B. Morgenstern, P. Meinicke (2008) Gene prediction in metagenomic fragments: a large scale machine learning approach. 2] K J. Hoff, T. Lingner, P. Meinicke, M. Tech (2009) Orphelia: predicting genes in metagenomic sequencing reads Nucleic Acids Research.

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