Atlas of alternative splicing profiles across animal tissues, cell types and developmental stages.

U12-type introns are spliced by the U12-dependent spliceosome and are present in the genomes of many higher eukaryotic lineages including plants, chordates and some invertebrates. Investigations into the evolution and mechanism of U12-depending splicing would be facilitated by access to a catalog of such introns. However, due to their relatively recent discovery and a systematic bias against recognition of non-canonical splice sites in general, the introns defined by U12-type splice sites are under-represented in genome annotations. Such under-representation compounds the already difficult problem of determining gene structures. It also impedes attempts to study these introns genome-wide or phylum-wide. The resource described here, the U12 Intron Database (U12DB), aims to catalog the U12 introns of completely sequenced eukaryotic genomes and associate orthologous introns with each other.

trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment It also includes readAl, a format converter between most alignment formats.

A set of very optimized tools for indexing/querying huge genomes/files. Provided so far: a very fast exact mapper, and an unconstrained split-mapper

The Flux Simulator aims at modeling RNA-Seq experiments in silico: sequencing reads are produced from a reference genome according annotated transcripts.

The Flux Capacitor predicts abundances for transcript molecules and alternative splicing events from RNAseq experiments. Additionally, there is a simulation pipeline that is capable to simulate whole transcriptome sequencing experiments.

T-Coffee is a multiple sequence alignment package. You can use T-Coffee to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle, etc.) into one unique alignment (M-coffee). T-Coffee can align Protein, DNA and RNA sequences. It is also able to combine sequence information with protein structural information (Expresso), profile information (PSI-Coffee) or RNA secondary structures (R-Coffee).

SymCurv is a computational ab initio method for nucleosome positioning prediction. It is based on the structural property of natural nucleosome forming sequences, to be symmetrically curved around a local minimum of curvature.

SuperFly is a database for the comparative analysis of segmentation gene expression and regulation in dipteran species (flies, midges, and mosquitoes)

Starcode is a DNA sequence clustering software. Sequence clustering is performed by finding all pairs below a Levenshtein distance metric. Typically, a file containing a set of related DNA sequences is passed as input, jointly with a parameter specifying the desired cluster distance. Starcode aligns and computes the distance between all the sequence pairs and prints a line for each cluster containing: canonical DNA sequence, sequence count and the list of sequences that belong to the cluster.

Starcode has many applications in the field of biology, such as DNA/RNA motif recovery, barcode clustering, sequencing error recovery, etc.