i-ADHoRe3.0
i-ADHoRe is a highly sensitive software tool to detect degenerated homology relations within and between different genomes.
Software
ISMAGS
This Cytoscape app provides a graphical interface for the ISMAGS algorithm.
ISMAGS can numerate all instances of a motif in a graph, making optimal use of the motif's symmetries.
LeMoNe
LeMoNe is a software package for Learning Module Networks from gene expression data.
MORPH
MORPH (“MOdule guided Ranking of candidate PatHway genes”) is an algorithm to associate candidate genes with a given target pathway. Unlike any other algorithm in plant sciences, MORPH tests multiple combinations by learning how to choose among various forms of evidence (large scale data sets) to link genes to a specific target pathway. It was shown that MORPH can detect metabolic pathways that leave a strong ‘signature’ in high throughput data sets. Then MORPH robustly predicted genes that where experimentally validated to be part of the specific metabolic pathway analyzed.
PlantCARE
PlantCARE is a database of plant cis-acting regulatory elements, enhancers and repressors. Regulatory elements are represented by positional matrices, consensus sequences and individual sites on particular promoter sequences. Links to the EMBL, TRANSFAC and MEDLINE databases are provided when available. Data about the transcription sites are extracted mainly from the literature, supplemented with an increasing number of in silico predicted data.
pppbenchmark
We present a large-scale benchmarking study of 17 state-of-the-art PPPs. A multi-faceted evaluation strategy is proposed that can be used as a gold standard for promoter prediction evaluation, allowing authors of promoter prediction software to compare their method to existing methods in a proper way. This evaluation strategy is subsequently used to compare the chosen promoter predictors, and an in-depth analysis on predictive performance, promoter class specificity, overlap between predictors and positional bias of the predictions is conducted.
ProSOM
ProSOM is a promoter prediction program based on unsupervised clustering of physical properties of DNA. The program can clearly distinguish between the structural profiles of promoter sequences and other genomic sequences by using self-organizing maps.
TAPIR
TAPIR is a web server designed for the prediction of plant microRNA targets. The server offers the possibility to search for plant miRNA targets using a fast and a precise algorithm. The precise option is much slower but guarantees to find less perfectly paired miRNA - target duplexes. Furthermore, the precise option allows the prediction of target mimics, which are characterized by a miRNA - target duplex having a large loop, making them undetectable by traditional tools.
