Browsing by Author "Messeguer, Xavier"

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  • ABS: a database of Annotated regulatory Binding Sites from orthologous promoters
    Blanco, Enrique; Farré, Domènec; Albà Soler, Mar; Messeguer, Xavier; Guigó Serra, Roderic (Oxford University Press, 2006)
    Information about the genomic coordinates and the sequence of experimentally identified transcription factor binding sites is found scattered under a variety of diverse formats. The availability of standard collections of ...
  • Evolution of Tandem Repeat Satellite Sequences in Two Closely Related Caenorhabditis Species. Diminution of Satellites in Hermaphrodites
    Subirana, Juan A.; Messeguer, Xavier (MDPI, 2017)
    The availability of the genome sequence of the unisexual (male-female) Caenorhabditis nigoni offers an opportunity to compare its non-coding features with the related hermaphroditic species Caenorhabditis briggsae; to ...
  • Fringe analysis of synchronized parallel algorithms on 2-3 trees
    Baeza Yates, Ricardo; Gabarró Vallès, Joaquim; Messeguer, Xavier (Springer, 1998)
    We are interested in the fringe analysis of synchronized parallel insertion algorithms on 2–3 trees, namely the algorithm of W. Paul, U. Vishkin and H. Wagener (PVW). This algorithm inserts keys into a tree of size n with ...
  • High evolutionary turnover of satellite families in Caenorhabditis
    Subirana, Juan A.; Albà Soler, Mar; Messeguer, Xavier (BioMed Central, 2015)
    Background. The high density of tandem repeat sequences (satellites) in nematode genomes and the availability of genome sequences from several species in the group offer a unique opportunity to better understand the ...
  • How long are long tandem repeats? a challenge for current methods of whole-genome sequence assembly: the case of satellites in caenorhabditis elegans
    Subirana, Juan A.; Messeguer, Xavier (MDPI, 2018)
    Repetitive genome regions have been difficult to sequence, mainly because of the comparatively small size of the fragments used in assembly. Satellites or tandem repeats are very abundant in nematodes and offer an excellent ...
  • Long non-coding RNAs as a source of new peptides
    Ruiz Orera, Jorge, 1988-; Messeguer, Xavier; Subirana, Juan A.; Albà Soler, Mar (eLife, 2014)
    Deep transcriptome sequencing has revealed the existence of many transcripts that lack long or conserved open reading frames (ORFs) and which have been termed long non-coding RNAs (lncRNAs). The vast majority of lncRNAs ...
  • Multiple non-collinear TF-map alignments of promoter regions
    Blanco, Enrique; Guigó Serra, Roderic; Messeguer, Xavier (BioMed Central, 2007)
    Background: The analysis of the promoter sequence of genes with similar expression patterns is/na basic tool to annotate common regulatory elements. Multiple sequence alignments are on the/nbasis of most comparative ...
  • Transcription factor map alignment of promoter regions
    Blanco, Enrique; Messeguer, Xavier; Smith, Temple F.; Guigó Serra, Roderic (Public Library of Science (PLoS), 2006)
    We address the problem of comparing and characterizing the promoter regions of genes with similar expression patterns. This remains a challenging problem in sequence analysis, because often the promoter regions of co-expressed ...
  • Translation of neutrally evolving peptides provides a basis for de novo gene evolution
    Ruiz-Orera, Jorge; Verdaguer-Grau, Pol; Villanueva Cañas, José Luis, 1984-; Messeguer, Xavier; Albà Soler, Mar (Springer, 2018)
    Accumulating evidence indicates that some protein-coding genes have originated de novo from previously non-coding genomic sequences. However, the processes underlying de novo gene birth are still enigmatic. In particular, ...
  • Uncovering de novo gene birth in yeast using deep transcriptomics
    Blevins, William Robert, 1987-; Ruiz Orera, Jorge, 1988-; Messeguer, Xavier; Blasco Moreno, Bernat, 1986-; Villanueva Cañas, José Luis, 1984-; Espinar, Lorena; Díez Antón, Juana, 1962-; Carey, Lucas, 1980-; Albà Soler, Mar (Nature Research, 2021)
    De novo gene origination has been recently established as an important mechanism for the formation of new genes. In organisms with a large genome, intergenic and intronic regions provide plenty of raw material for new ...