REALPHY.UNIBAS.CH

REALPHY Online Tool

Swiss Institute of Bioinformatics. Build separate phylogeny for each reference alignment. Min per base coverage. Frederic Bertels, Olin K. Silander, Mikhail Pachkov, Paul B. Rainey, and Erik van Nimwegen. Automated reconstruction of whole genome phylogenies from short sequence reads. Molecular Biology and Evolution; Published online 5 March 2014. Escherichia coli from Touchon et al. 2009. Results for all 21 references. Results after reference alignment merging. Results after reference alignment merging.

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REALPHY Online Tool | realphy.unibas.ch Reviews

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Swiss Institute of Bioinformatics. Build separate phylogeny for each reference alignment. Min per base coverage. Frederic Bertels, Olin K. Silander, Mikhail Pachkov, Paul B. Rainey, and Erik van Nimwegen. Automated reconstruction of whole genome phylogenies from short sequence reads. Molecular Biology and Evolution; Published online 5 March 2014. Escherichia coli from Touchon et al. 2009. Results for all 21 references. Results after reference alignment merging. Results after reference alignment merging.

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2 project name

3 merge reference alignments

4 advanced options

5 read length

6 seed length

7 min phred quality

8 polymorphism threshold

9 gap threshold

10 genes only

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email,project name,merge reference alignments,advanced options,read length,seed length,min phred quality,polymorphism threshold,gap threshold,genes only,bowtie2 parameters,bowtie2 documentation,phyml parameters,phyml documentation,reference genomes,manual

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REALPHY Online Tool | realphy.unibas.ch Reviews

https://realphy.unibas.ch

Swiss Institute of Bioinformatics. Build separate phylogeny for each reference alignment. Min per base coverage. Frederic Bertels, Olin K. Silander, Mikhail Pachkov, Paul B. Rainey, and Erik van Nimwegen. Automated reconstruction of whole genome phylogenies from short sequence reads. Molecular Biology and Evolution; Published online 5 March 2014. Escherichia coli from Touchon et al. 2009. Results for all 21 references. Results after reference alignment merging. Results after reference alignment merging.

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swissregulon.unibas.ch

SwissRegulon

http://swissregulon.unibas.ch/fcgi/sr/documentation

Swiss Institute of Bioinformatics. Search mammal promoters and motifs:. Prediction of transcription factor binding sites with Motevo algorithm:. Finding regulatory elements and regulatory motifs: a general probabilistic framework. 2007 Sep 27; 8 Suppl 6:S4. Annotating of promoteroms (transcription start sites, transcription start clusters and transcription start regions):. Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data.

swissregulon.unibas.ch

SwissRegulon

http://swissregulon.unibas.ch/fcgi/sr/fantom4

Swiss Institute of Bioinformatics. Motevo predictions for CAGE promoters. Motevo predictions for REFSEQ promoters. Regulatory motifs (weight matrices). Association of regulatory motifs with TFs. Predicted regulatory edges for CAGE promoters. Predicted regulatory edges for REFSEQ promoters. Multispecies alignments of CAGE promoters. Multispecies alignments of REFSEQ promoters.

swissregulon.unibas.ch

SwissRegulon

http://swissregulon.unibas.ch/fcgi/sr/swissregulon

Swiss Institute of Bioinformatics. Search mammal promoters and motifs:. Swissregulon Database contains genome-wide annotations of regulatory sites. The predictions are based on Bayesian probabilistic analysis of a combination of input information including:. Experimentally determined binding sites reported in the literature. Known sequence-specificities of transcription factors. ChIP-chip and ChIP-seq data. Alignments of orthologous non-coding regions. Predictions were made using the PhyloGibbs.

swissregulon.unibas.ch

SwissRegulon

http://swissregulon.unibas.ch/fcgi/sr/publications

Swiss Institute of Bioinformatics. The transcriptional landscape of the mammalian genome. P Carninci, T. Kasukawa, S. Katayama, J. Gough, M. Frith, N. Maeda, R. Oyama, T. Ravasi, B. Lenhard, C. Wells and others. Science, 2005, 309(5740), 1559- 1563. PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. R Siddharthan, E. Siggia and E. Van Nimwegen. PLoS computational biology, 2005, 1(7), e67. Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes.

swissregulon.unibas.ch

SwissRegulon

http://swissregulon.unibas.ch/fcgi/sr/annotations

Swiss Institute of Bioinformatics. Search mammal promoters and motifs:. Select species to view in Genome Browser.

swissregulon.unibas.ch

SwissRegulon

http://swissregulon.unibas.ch/fcgi/sr/downloads

Swiss Institute of Bioinformatics. Motevo predictions of binding sites. Regulatory motifs (weight matrices). Association of regulatory motifs with TFs. Motevo predictions of binding sites. Regulatory motifs (weight matrices). Association of regulatory motifs with TFs. Motevo predictions of binding sites. Regulatory motifs (weight matrices). Association of regulatory motifs with TFs. Motevo predictions of binding sites. Regulatory motifs (weight matrices). Association of regulatory motifs with TFs.

swissregulon.unibas.ch

SwissRegulon

http://swissregulon.unibas.ch/fcgi/sr/software

Swiss Institute of Bioinformatics. The DWT-toolbox is a collection of software tools for performing motif finding and transcription factor binding site (TFBS) predictions with Dinucleotide Weight Tensors (DWTs). Besides a motif finder, and a program for predicting TFBSs with a given DWT in a given set of sequences, the toolbox also includes a program for constructing dilogos that visualize DWT motifs. PhyloGibbs is an algorithm for discovering regulatory sites in a collection of DNA sequences, including ...

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REALPHY Online Tool

Swiss Institute of Bioinformatics. Build separate phylogeny for each reference alignment. Min per base coverage. Frederic Bertels, Olin K. Silander, Mikhail Pachkov, Paul B. Rainey, and Erik van Nimwegen. Automated reconstruction of whole genome phylogenies from short sequence reads. Molecular Biology and Evolution; Published online 5 March 2014. Escherichia coli from Touchon et al. 2009. Results for all 21 references. Results after reference alignment merging. Results after reference alignment merging.

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