Services: Genes And Genomes

Providing a data and information resource for individual plant species

Plant-oriented online resource for comparative, evolutionary and functional genomics.

Tool for prediction of disease related mutations in proteins. Tool version 2 (PredictSNP 2) for prediction of disease related mutatins within human genome available since 2016.

Primer3 is a program for designing PCR primers and oligos. 

RNA-Seq Analysis Pipeline

A cloud computing web application implementing a complete and modular RNA-Seq analysis workflow.

Exploring and evaluating NGS data utilizing a modular programming structure allowing easy plugins.

A database annotating organellar RNA editing processes in their biological context.

A database of RNA editing events in humans from RNA-Seq and DNA-Seq data.

Python scripts developed with the aim to study RNA editing at genomic scale by next generation sequencing data.

ReferenceSeeker determines closely-related reference genomes following a scalable hierarchical approach. It combines a fast kmer profile-based database lookup of candidate reference genomes and subsequent computation of specific average nucleotide identity (ANI) values.

Tools to analyse cis-regulatory elements in genome sequences

Set of tools and a web server for complex characterization of repetitive DNA based on data from next generation of sequence reads.

The REPET package integrates bioinformatics pipelines dedicated to detecte, annotate and analyse transposable elements (TEs) in genomic sequences. The main pipelines are (i) TEdenovo, which search for interspersed repeats, build consensus sequences and classify them according to TE features, and (ii) TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations exported into GFF3 files.

The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs).

Providing access to many NGS and RNA tools, visualisations, interactive environments (e.g. IPython) as well as various utilities, reference genomes and data libraries.

End-to-end gene-level RNA-Seq differential expression workflow using Bioconductor packages. Starting from the FASTQ files are aligned to the reference genome, and a count matrix which tallies the number of RNA-seq reads/fragments within each gene for each sample is prepared. Performance of exploratory data analysis (EDA) for quality assessment and exploration of the relationship between samples, performance of differential gene expression analysis, and visual exploration of the results.

RnBeads is an R package for analysing DNA methylation data obtained with an experimental protocol that provides single-CpG resolution. 

Roddy is a framework for large scale NGS processing pipelines on Petabyte scale. It is used for the management of workflows in the Pan-Cancer Analysis of Whole Genomes (PCAWG) project.

Web tool for prediction of rRNA secondary structures.

A framework for software development in bioinformatics. It covers three aspects:.

1. Workflow wrapping the TF text-mining results from https://github.com/fnl plus other databases. 
2. High Throughput Sequencing related functionalities.
3. Rbbt wrapper for the Variant Effect Predictor.

Auto-downloads and installs the software.

A comprehensive data resource for salmonids species based on different omics data

A database with high-quality curated and freely accessible SARS-CoV-2 genomics- and contextual resources.

SIAMCAT is a modular framework for the statistical inference of associations between microbial communities and host phenotypes, such as disease states in clinical case-control studies. SIAMCAT is based on LASSO models, which offer distinctive advantages for model interpretation and microbial biomarker selection and avoid overfitting issues that can arise in naive combinations of feature selection and cross-validation. Part of the Microbiome Analysis Toolbox. 

SIDER is a web-based resource that contains information on marketed medicines and their recorded adverse drug reactions. This information is extracted from public documents and package inserts. SIDER makes available side effect frequency, drug and side effect classifications as well as links to further information, for example drug–target relations. It currently covers associations between 5,868 side effects and 1,430 drugs. Part of the Human Omics Analysis Toolbox. 

SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).

Data Analysis service for ribosomal RNA

SNPmasker is a program to mask all SNPs in given sequence using information of dbSNP. Additionally it is possible to mask all non-unique words using GenomeMasker module.

A database of RNA-binding splicing regulatory proteins reporting functional domains, protein and chemical interactors and expression data.

SQANTI3 is the first module of the [Functional IsoTranscriptomics (FIT)](https://tappas.org/) framework, which also includes IsoAnnot and tappAS.

Nextflow pipeline for splicing quantitative trait loci (sQTL) mapping based on sQTLseekeR2, performing the following analysis steps:

1. Index the genotype file
2. Preprocess the transcript expression data
3. Test for association between splicing ratios (a multivariate phenotype) and genetic variants in cis (nominal pass)
4. Obtain an empirical P-value for each phenotype (permutation pass, optional)
5. Control for multiple testing.