cinper

CINPER is an interactive knowledge-based web system to assist a biologist user to build in an intuitive manner a user-selected gene network for a prokaryotic organism, based on the information provided by the user, including (not necessarily all) annotated functions of genes and predicted operons in the target genome, protein-protein interactions, phylogenetic profiles, microarray gene-expression data, relevant pathway information from related organisms, and any information that the user may have about specific genes involved in the target network.

dbCAN

dbCAN is a database resource providing easy and convenient access to the sequences, alignments, hidden markov models (HMMs) and phylogenies of CAZy related enzyme families and functional modules. dbCAN is based on the sequence classification from the CAZy database and has the following functionalities

seas

SEAS is a computational tool for pathway enrichment analysis over a given set of genes in a specified organism against the pathways (or subsystems) in the SEED database, a popular pathway database for bacteria. SEAS maps a given set of genes of a bacterium to pathway genes covered by SEED through gene ID and/or orthology mapping, and then calculates the statistical significance of the enrichment of each relevant SEED pathway by the mapped genes. Our evaluation of SEAS indicates that the program provides highly reliable pathway mapping results and identifies more organism-specific pathways than similar existing programs.

kobas2

KOBAS 2.0 is a web server that annotates an input set of genes with putative pathways and disease relationships based on mapping to genes with known annotations. It allows for both ID mapping and cross-species sequence similarity mapping. It then performs statistical tests to identify statistically significantly enriched pathways and diseases. KOBAS 2.0 incorporates knowledge across 1327 species from 5 pathway databases (KEGG PATHWAY, PID, BioCyc, Reactome and Panther) and 5 human disease databases (OMIM, KEGG DISEASE, FunDO, GAD and NHGRI GWAS Catalog).

kobas1

KOBAS (KO-Based Annotation System (KOBAS) 1.0 is a standalone console application that can automatically annotate a set of sequences with KO terms and identify both the most frequent and the statistically significantly enriched pathways. Results from both whole genome and microarray gene cluster annotations with KOBAS are comparable and complementary to known annotations. KOBAS is a freely available stand-alone Python program that can contribute significantly to genome annotation and microarray analysis.