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Tancred Frickey & Georg Weiller
The aim of Affytrees is to provide a quick and easy way for plant scientists to determine which of their genes of interest have orthologues on any of the other affymetrix plant chips. To this effect, the web-server provides BLAST results, alignments and phylogenetic trees for the consensus sequences of affymetrix chips for specific species.
Batch submission as well as more complex queries than simple orthology are possible.
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Nicolas Goffard & Georg Weiller
GeneBins provides resources to interpret gene expression results from microarray experiments
We developed a bioinformatics system to assign probe set sequences of any organism to a hierarchical functional classification ('BINs') modelled on KEGG ontology.
The GeneBins database currently supports the functional classification of expression data from 4 plant Affymetrix GeneChips; Arabidopsis thaliana, the model legumes: Medicago truncatula (barrel medic) and Glycine max (soybean), and Oryza sativa (rice).
Based on these assignments, on online analysis tool is available to interpret gene expression from microarray experiments by identifying most relevant pathways involved. We also applied this system to extend MapMan software to any organism without being restricted to sequence similarity with Arabidopsis.
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Jiayu Wen, Tancred Frickey, Georg Weiller
Medicago-MIRATdb is an open access resource of candidate miRNA and target genes for the model legume Medicago truncatula.The aim of Medicago-MIRATdb is to provide the research community with a resource
of putative M. truncatula miRNAs, their potential target genes, and other supporting information from our in-house analysis to assist in the selection of candidate miRNAs and target genes for experimental design. The database currently contains 17,175 predicted miRNAs and their 3,331 unique precursor regions as well as the 16,734 genes potentially targeted by these miRNAs. While most of these miRNAs are predicted from introns, 445 are on the exons of 88 non-coding RNA transcripts.
The database provides detailed information on the sequences of the predicted miRNAs, their precursors and target genes as well as the alignments of the miRNA::miRNA* and miRNA::target duplexes, and sequence source information such as the EST library, tissue category, and EST clone number. Information about miRNA conservation in other plant species, functional classification of the target genes, and clusters of similar miRNA are also provided. The web-interface of the database affords flexibility in both search and download choices for miRNAs or target genes of interest to assist in miRNA experimental design.
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Tancred Frickey & Georg Weiller
Mclip is a tool for motif-elucidation in DNA/RNA-sequences. Although there are a large number of motif-detection tools around, most require "nuisance" parameters to be specified (i.e. things you would like the program to tell you, not the other way around), such as the exact width of the motif you are searching for, or how often it will be present in the set of sequences you supplied.
Quite a few program will also return the best motif only, without any estimate of how good the second best would have been, or provide cryptic statistical estimates for the "quality" of detected motifs.
Mclip uses a deterministic, expectation-maximization approach to motif detection that can find gapped motifs and provides a P-value or E-value estimate for each motif found in a sequence.
Mclip is a Java program and should run mith minimal hassle on most computers. Only prerequisite is that a Java1.5 or better runtime environment be available (which you can download HERE)
The program is available for free download under the GNU-GPL HERE; source code is included in the archive.
For motif detection in small sets of sequences a web-interface is available HERE
Further information is available HERE
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Nicolas Goffard & Georg Weiller
PathExpress is a web-based tool developed to interpret gene expression data obtained from microarray experiments by identifying the most relevant metabolic pathways associated with a list of genes (e.g. differentially expressed). A graphical pathway representation permits the visualisation of the expressed genes in a functional context. Based on the publicly accessible KEGG Ligand database, PathExpress can be adapted to any organism and is currently available for seven Affymetrix genome arrays. About 20% of the probe sets of each array have been assigned to EC numbers by homology relationship and linked to corresponding metabolic pathways.
PathExpress is available at: http://bioinfoserver.rsbs.anu.edu.au/utils/PathExpress/
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