We have developed the WALTZ algorithm for the identification of amyloid forming hexapeptides in amino acid sequences. WALTZ combines terms from amino acid sequence scoring in the learning set, physical property analysis and homology modelling. The method shows ~84% sensitivity at ~92% specificity on the AmylHex dataset, and correctly identifies mutations in human proteins known to be associated with amyloid deposition. The combination of the aggregation predicting algorithm TANGO with WALTZ, provides a complete cover of aggregation and amyloid tendency in protein sequences.
WALTZ is being developed by Joost Schymkowitz and Frederic Rousseau and their team at the SWITCH Laboratory of VIB in Brussels, Belgium, in collaboration with Luis Serrano and his team at the CRG in Barcelona, Spain.
The resource described, the U12 Intron Database (U12DB), aims to catalog the U12 introns of completely sequenced eukaryotic genomes and associate orthologous introns with each other.
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.
Toni Gabaldón
Category:
Sequence Analysis
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.
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.
