Analysis Tools
Simap
Description Simap
Gepard
Gepard (German: "cheetah", Backronym for "GEnome PAir - Rapid Dotter") allows the calculation of dotplots even for large sequences like chromosomes or bacterial genomes.
MetaP
metaP-Server is a web-based data analysis tool for quantitative metabolomics data. The server provides automated and standardized analyses such as data quality checks, principal component analysis, hypothesis tests, and mapping of metabolites onto colored KEGG pathways aiming at facilitating the exploration and biological interpretation of data from metabolomics experiments.
MDCS
The MDCS provides maximal margin Linear Programming method (Antonov et al., 2004) for classification of tumor samples based on microarray data. This procedure detects groups of genes and constructs models (features) that strongly correlate with particular tumor types. The detected features include genes whose functional relations are changed for particular cancer types.
Eclat
Eclat s a server for the classification of ESTs from mixed EST pools (e.g., from fungus infected plants) for determination of the EST's origin. It is based on the machine learning algorithm Support Vector Machines and uses codon frequencies for discrimination between plant and fungal origin.
Est3
EST3 is a server developed to classify EST sequences from host-pathogen interface using frequency of nucleotide triplets. Compared to the ECLAT it includes much larger number of genome pairs and use triplets rather than codon usage. This allows to skip identification of CDS regions and make possible classification of EST sequences containing non-coding UTR data.
Spc
This program performs clustering of data using properties of paramagnetic systems. It also provides visualization of calculated clusters.
BFAB
BFAB collects ressources that can be used to benchmark and to develop new sequence annotation methods. The manual annotation data of four bacterial genomes, Bacillus subtilis, Helicobacter pylori, Listeria innocua and Listeria monocytogenes as well as some sequence parameters are available in XML format for download. The annotation of BFAB dataset was manually performed using FunCat (Ruepp et al, 2004).
BioRel
BIOREL is a web-based resource for quantitative estimation of the gene network bias in relation to available database information about gene activity/function/properties/associations/interactions. BIOREL infers the bias/relevance score, which shows the correspondence between gene associations in the network and information extracted from different biological databases. BIOREL provides standardized estimations of the network biases extracted from independent data.
VCCLAB
Free on-line calculation of lipophilicity, logP, aqueous solubility, logS, molecular indices using Java applets. Analysis methods include neural networks, partial least squares and unsupervised forward selection.
Funat
FUNAT uses descriptors were derived from sequence alignment scores, InterPro domains, synteny information, lengths of sequences, and calculated protein properties to provide functional annotation of new protein sequences using FunCat (Ruepp et al, 2004). It provides both on-line interactive annotation as well as web services.
OCHEM
The OCHEM is an online database with the modeling environment. It is a further development of the VCCLAB. OCHEM allows to submit experimental data, use them and/or data provided by other users to build predictive QSAR models for physical-chemical or biological properties. A larger variety of methods and descriptors (both public and commercial ones) is available. The data and models developed and published at OCHEM are publicly available and can be accessed on-line by other users.
Phenomir
The PhenomiR database provides information about differentially regulated miRNA expression in diseases and other biological processes.
Contar
Multi-tool target prediction of zebrafish miRNA targets, consensus targets.
miTALOS
With miTALOS you can visualize and analyze microRNA pathway associations.
ZfishDb
The ZebraFish Interaction SearcH DataBase(ZFISHDB) retrieves Danio rerio gene interactions from interactions between orthologous genes.