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

AStalavista, the Alternative Splicing Transcriptional Landscape Visualization Tool.

Type:
Application/Software

AStalavista, the Alternative Splicing Trascriptional Landscape Visualization Tool and more, retrieves all alternative splicing events from generic transcript annotations.

Website:
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Type:
Application/Software

compmerge is a program that tries to solve the same problem as cuffmerge. It is not limited to cufflinks/stringtie models and transcripts, but can work with any GTF file. It merges the spliced transcripts that have a compatible intron structure and merges the monoexonic transcripts based on simple stranded overlap.The output is a GTF file of merged transcripts.

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CRISPETa is a flexible tool to design optimal pairs of sgRNAs for deletion of desired genomic regions.

Type:
Application/Software, Webservice

CRISPETa is a flexible tool to design optimal pairs of sgRNAs for deletion of desired genomic regions. These target regions can be supplied in BED or UCSC format. CRISPETa can be run on any number of targets - from one to thousands.

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The transcriptome project aims to sequence various cell lines, and within those cell lines, different compartments, and RNA fractions, using different technologies.

Category:
Gene Analysis

The transcriptome project aims to sequence various cell lines, and within those cell lines, different compartments, and RNA fractions, using different technologies.

Website:

Type:
Application/Software

GEM-Tools is a C API and a Python module to support and simplify usage of the GEM Mapper (https://bio.tools/tool/crg.eu/The%20GEM%20%28GEnome%20Multi-tool%29%20Li...)

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Geneid is an ab initio gene finding program used to predict genes along DNA sequences in a large set of organisms.

Category:
Gene Analysis
Type:
Application/Software, Webservice

Geneid is an ab initio gene finding program used to predict genes along DNA sequences in a large set of organisms. The program can be run through a web server (http://genome.crg.es/software/geneid/geneid.html) or downloaded and executed by command line

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Type:
Application/Software

GenNon-h is a software designed to generate multiple sequence alignments of DNA evolving on any phylogenetic tree.

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gff2aplot is a program to visualize the alignment of two sequences together with their annotations.

Type:
Application/Software

 Input for the program consists of single or multiple files in GFF-format which specify the alignment coordinates and annotation features of both sequences. Output is in PostScript format of any size. The features to be displayed are highly customizable to meet user specific needs. The program serves to generate print-quality images for comparative genome sequence analysis.

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gff2ps is a program for visualizing annotations of genomic sequences.

Type:
Application/Software

gff2ps is a program for visualizing annotations of genomic sequences. The program takes the annotated features on a genomic sequence in GFF format as input, and produces a visual output in PostScript. While it can be used in a very simple way, it also allows for a great degree of customization through a number of options and/or customization files.

Website:
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gff2ps is a program for visualizing annotations of genomic sequences

gff2ps is a program developed at Fundació Institut Mar d’Investigacions Mèdiques (IMIM) in collaboration with CRG (Roderic Guigó group), to visualize annotations of genomic sequences. The program takes as input the annotated features on a genomic sequence in GFF format, and produces a visual output in PostScript. It can be used in a very simple way, because it assumes that the GFF file itself carries enough formatting information, but it also allows through a number of options and/or a configuration file, for a great degree of customization.

For more information about this software, please click here

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