Datasets

Relevant information on datasets and similar resources

lncRNA data files

LncRNA Data Page

On this page you will find various data files relating to our work on lncRNA. 

Please note:

1) All coordinates refer to human genome version GRCh37 (hg19).

2) The genesets here are all from GENCODE version 7.

3) Original GENCODE annotations can be found here: http://www.gencodegenes.org/releases/7.html

 

Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes (2010) Bioinformatics (Oxford, England)

Here you have the full article in pdf:  http://bioinformatics.oxfordjournals.org/content/early/2010/09/21/bioinformatics.btq516.full.pdf? ijkey=SoZbNas3eLI6Jzu&keytype=ref

Model fitting for mixture models

Phylogenetic data arising on different tree topologies might be mixed on a given alignment. Models taking into it account usually contain a large number of parameters and the usual tests for model fitting cannot deal with them. Here we discuss an approach for model fitting of algebraic models on m-tree mixtures. This is joint work in progress with Marta Casanellas and Jesus Fernandez-Sanchez

BMC Bioinformatics: Multiple Non-Collinear TF-map Alignments of Promoter Regions

Contents

U12DB: a database of orthologous U12-type spliceosomal introns

U12DB: The U12 Intron Database

PLoS Computational Biology (2006): Transcription Factor Map Alignment of Promoter Regions

Genome Biology (2006): EGASP: The human ENCODE GENOME ANNOTATION ASSESSMENT PROJECT

SUPPLEMENTARY MATERIALS FOR

 

Nucleic Acids Research (2005): Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes

Comparative gene finding in chicken indicatesthat we are closing in on the set ofmulti-exonic widely expressed human genes R. Castelo*, A. Reymond, C. Wyss, F. Câmara, G. Parra, S.E. Antonarakis, R. Guigó and E. Eyras

Bibliography

Genome Research (2005): Comparison of Splice Sites in Mammals and Chicken

SUPPLEMENTARY MATERIALS FOR

"Comparison of Splice Sites in Mammals and Chicken"

J. F. Abril, R. castelo, and R. Guigó *.

Bioinformatics (2004): Splice site identification by idlBNs

Splice Site Identification by idlBNs R. Castelo* and R. Guigó Bioinformatics, 20(1):i69-i76, 2004 [full text]

Science (2003): Selenoprotein gene prediction in Human

Characterization of mammalian selenoproteomes G. V. Kryukov, S. Castellano, S. V. Novoselov, A. V. Lobanov, O. Zehtab, R. Guigó and V. N. Gladyshev*.

PNAS (2003): Comparison of human and mouse genomes followed by experimental validation

SUPPLEMENTARY MATERIALS FOR Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes

Genome Research (2003): Comparative Gene Prediction in Human and Mouse

SUPPLEMENTARY MATERIALS FOR Comparative gene prediction in human and mouse

Genome Research (2000): Gene Prediction Programs Evaluation in Large DNA Sequences

"An Assessment of Gene Prediction Accuracy in Large DNA Sequences." R. Guigó, P. Agarwal, J.F. Abril, M. Burset and J.W. Fickett. Genome Research 10(10):1631-1642 (2000).

 

Genome Research (2000): geneid in Drosophila melanogaster

"Geneid in Drosophila." G. Parra, E. Blanco, and R. Guigó. Genome Research 10(4):511-515 (2000).

Genomics (1996): Evaluation of gene structure prediction programs

"Evaluation of gene structure prediction programs." M. Burset and R. Guigó. Genomics, 34:353-357 (1996).

 

EMBO reports (2001): Selenoprotein gene prediction in the Fly

in silico identification of novel selenoproteins in the Drosophila melanogaster genome S. Castellano, N. Morozova, M. Morey, M.J. Berry, F. Serras, M. Corominas and R. Guigó*.

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