Tools
PALO
Developed by the Evolutionary Genomics group, Protein ALignment Optimiser (PALO) is an algorithm for the selection of the best combination of protein isoforms among orthologous genes in the construction of a multiple alignment. You can easily upload your files from ENSEMBL and this tool will tell you which is the most suitable combination for you to align.
iso-kTSP
This program runs the kTSP classification algorithm giving both intermediate results and a final prediction model. There are options to perform the analysis on alternative splicing isoforms and to test an already defined kTSP model (of genes or isoforms) against a dataset. Developed by the Computational RNA Biology group.
BeFree
Developed by the Integrative Bioinformatics group, BeFree is a text mining tool to unlock the information contained in biomedical documents. It is composed of the Biomedical Named Entity Recognition (BioNER) module based on dictionaries using fuzzy- and pattern matching methods to find and uniquely identify entity mentions in the literature, and a module for Relation Extraction (RE) based on Support Vector Machine (SVM).
ArchDB
Developed by the Structural Bioinformatics group, ArchDB is a structural classification of loops extracted from known protein structures, based on the geometry and conformation of the loop. The geometry is defined by four internal variables and the type of regular flanking secondary structures, resulting in 10 different loop types.
BIANA
Developed by the Structural Bioinformatics group, BIANA (Biologic Interactions and Network Analysis) is a biological database integration and network management framework written in Python that uses a high level abstraction schema to define databases providing any kind of biological information (both individual entries and their relationships).
STScan
Developed by the Computational RNA Biology group, STScan is a tool for the prediction of RNA:RNA interactions.
VariantFiltering
Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc. Developed by the Functional Genomics group.
PharmaTrek
Developed by the Systems Pharmacology group, PharmaTrek allows pharmacological space to be navigated in a flexible and interactive way, by accessing the content of ChEMBL via the Open PHACTS Discovery Platform. The results of a target search are highly filterable and easily linked with ligand chemical structure.
Pyicoteo
Developed by the Computational RNA Biology group, Pyicoteo is a suite of tools for the analysis of high-throughput sequencing data. It works with genomic coordinates, it was mainly developed for Illumina mapped reads, but it's platform-agnostic, since in many cases, it simply works with genomic coordinates.
GSVA
Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. Developed by the Functional Genomics group.
