Computational Biology of RNA Processing

Computational Biology of RNA Processing

Bioinformatics and Genomics

Computational Biology of RNA Processing

Group leader
j

Computational Biology of RNA Processing

Group leader
j

1988 Ph.D. in Statistics. Universitat de Barcelona. (Spain).
1988-1993 Postdoctoral researcher at the Molecular Biology Computer Research Resource. Dana Farber Cancer Institute, Harvard University (Division of Biostatistics) BioMolecular Engineering Research Center. Boston University and Theoretical Biology And Biophysics Group (Los Alamos national Laboratory).
Since 1994 Investigator at Institut Municipal d’Investigació Mèdica (IMIM). Barcelona, (Spain).
Since 2001 Associate Professor at the Universitat Pompeu Fabra and coordinator of the Bioinformatics Programme at the Centre de Regulació Genòmica, Barcelona, (Spain).

 Group News

Genome Editing: Pressing the «Delete» Button on DNA (02/03/2017)
Until recently, genomics was a «read-only» science. But scientists led by Rory Johnson at the University of Bern and the Centre for Genomic Regulation in Barcelona, have now developed a tool for quick and easy deletion of DNA in living cells. This software will boost efforts to understand the vast regions of non-coding DNA, or «Dark Matter», in our DNA and may lead to discovery of new disease-causing genes and potential new drugs.

Spanish scientists sequence the genome of the Iberian lynx, the most endangered felid (14/12/2016)
Genomic analysis of the Iberian lynx confirms that it is one of the species with the least genetic diversity among individuals, which means that it has little margin for adaptation.

The Blueprint project celebrates major manuscript release (18/11/2016)
BLUEPRINT scientists, including researchers at the Centre for Genomic Regulation, release a collection of 25 publications in Cell, Cell Press-associated and other high-impact journals. These are part of a package of 41 publications by the International Human Epigenome Consortium (IHEC) of which BLUEPRINT is a member.

'Blueprint' study of epigenetics of blood cells will serve biology and medicine (07/09/2016)
Researchers from the EU-funded BLUEPRINT project join their international colleagues this week at the 2016 International Human Epigenome Consortium (IHEC) conference in Brussels to report the latest results in understanding blood cell development and blood disease.

CRG researchers contribute to the sequencing of the Turbot genome (09/03/2016)
The first vertebrate to be genetically sequenced in Spain, the Turbot (Scophthalmus maximus), has a much more refined visual system than other fish as it has evolved to adapt to the shortage of light of the seabed. In addition, the fat in its cell membranes are far higher than in other species to withstand the low water temperatures in its habitat.

The mesoamerican bean genome decoded (25/02/2016)
An Ibero-American team of scientists decoded the Mesoamerican variety of the bean genome coinciding with the celebration of the International Year of Pulses, as designated by the United Nations.

Summary

Research in our group focuses on the investigation of the signals involved in gene specification in genomic sequences (promoter elements, splice sites, translation initiation sites, ...). We are interested both in the mechanism of their recognition and processing, and in their evolution. In addition, but related to this basic component of our research, our group is also involved in the development of software for gene prediction and annotation in genomic sequences. Some of our current projects are:

  • Evaluation of Gene Prediction Programmes
  • Gene Prediction software: geneid
  • Genome-Wide Search for Selenoproteins
  • Gene Prediction by Comparative Genomics
  • Splicing
  • Gene Structure Evolution
  • Phylogenetic Reconstruction

See also the Roderic Guigó lab website

SECISaln will predict a SECIS element in the query sequence, split it into its constituent parts and align these against a precompiled database of eukaryotic SECIS elements.

Category:
Sequence Analysis
Type:
Webservice

SECISaln will predict a SECIS element in the query sequence, split it into its constituent parts and align these against a precompiled database of eukaryotic SECIS elements.

Website:
Contact person:

In this web server we provide public access to two new computational methods for selenoprotein identification and analysis:

Type:
Webservice

In this web server we provide public access to two new computational methods for selenoprotein identification and analysis: SECISearch3 replaces its predecessor SECISearch as a tool for prediction of eukaryotic SECIS elements. Seblastian is a new method for selenoprotein gene detection that uses SECISearch3 and then predicts selenoprotein sequences encoded upstream of SECIS elements. Seblastian is able to both identify known selenoproteins and predict new selenoproteins. This project is the result of a collaboration with Vadim Gladyshev's lab in Harvard

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Selenoprofiles is a homology-based gene finding tool which is suitable for selenoprotein prediction in large nucleotide databases, like genomes.

Category:
Gene Analysis
Type:
Application/Software

Selenoprofiles is a homology-based gene finding tool which is suitable for selenoprotein prediction in large nucleotide databases, like genomes. Selenoproteins are a group of proteins that contain selenocysteine (Sec), a rare amino acid inserted co-translationally into the protein chain. The Sec codon is UGA, which is normally a stop codon. In selenoproteins UGA is recoded to Sec in presence of specific signals on selenoprotein gene transcripts. Due to the dual role of the UGA codon, selenoprotein prediction and annotation are difficult tasks and are left mostly to manual analysis, since there are no reliable “golden standard” programs for this purpose. Here we present an homology-based in silico tool to scan genomes for members of the known selenoprotein families: selenoprofiles. This pipeline has features that make it suitable for selenoprotein prediction, and is shown to correctly predict selenoproteins that are badly annotated in Ensembl. Selenoprofiles is a python-built pipeline that internally runs psitblastn, exonerate, genewise and SECISearch.

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sgp2 is a program to predict genes by comparing anonymous genomic sequences from different species.

Type:
Application/Software, Webservice

sgp2 is a program to predict genes by comparing anonymous genomic sequences from different species. It combines tblastx, a sequence similarity search program, with geneid, an ab initio gene prediction program.

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Type:
Application/Software

SJcount is a utility for fast SJ (splice-junction) quantification. It is an annotation-agnostic offset-aware version of bam2ssj

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Type:
Webservice

model Selection in Phylogenetics based on algebraic INvariants

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Type:
Application/Software

sQTLseekeR is a R package to detect splicing QTLs (sQTLs), which are variants associated with change in the splicing pattern of a gene. Here, splicing patterns are modeled by the relative expression of the transcripts of a gene.

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SymCurv is a computational ab initio method for nucleosome positioning prediction.

Type:
Application/Software

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.

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The Flux Capacitor predicts abundances for transcript molecules and alternative splicing events from RNAseq experiments.

Type:
Application/Software

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.

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Type:
Application/Software

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

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