CARMO is a web-based platform providing comprehensive annotations for multi-omics data, including transcriptomic data sets, epi-genomic modification sites, SNPs from genome re-sequencing, and the large gene lists derived from these omics studies.
eGATU (easy Genome Annotation Transfer Utility) is a light application modelled on GATU. It allows users to transfer annotations to an input genome without having to specify a reference.
GATU (Genome Annotation Transfer Utility) annotates a genome based on a very closely related reference genome. The proteins/mature peptides of the reference genome are BLASTed against the genome to be annotated in order to find the genes/mature peptides in the genome to be annotated.
BASys (Bacterial Annotation System) is a web server that supports automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences.
ClueGO is a Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network and it can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easely extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be fused to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role.
The est2assembly platform is the only platform for standardising transcriptome projects: go from raw trace files to an annotated GBrowse interface driven by the Seqfeature database. It accepts both Sanger and 454 sequencing technology for a denovo assembly, annotation and data mining of EST data.
RNAspace is a platform which aims at providing an integrated environment for non-coding RNA annotation. The platform allows running in an integrated environment a variety of ncRNA gene finders, to explore results with dedicated tools for comparison, visualization and edition of putative ncRNAs and to export them in various formats
ProSAT toolkit is a set of programs that allow building SVM based models for annotating amino acid residues in protein sequences using user supplied features (like PSI-BLAST profiles, or PSIPred profiles). In particular, the toolkit builds features using a window around the residue, and is equipped with a specialized kernel function (normalized second order exponential kernel function nsoe ) along with the standard svm kernel function.
:: DEVELOPER
Professsor Huzefa Rangwala (rangwala@cs.gmu.edu) and Professsor George Karypis
RAMMCAP is a metagenomic analysis package developed using an ultra-fast sequence clustering algorithm, fast protein family annotation tools, and a novel statistical metagenome comparison method that employs a unique graphic interface. RAMMCAP processes extremely large datasets with only moderate computational effort.