Now showing items 21-31 of 31

    • How long are long tandem repeats? A challenge for current methods of whole-genome sequence assembly: The case of satellites in caenorhabditis elegans 

      Subirana Torrent, Juan A.; Messeguer Peypoch, Xavier (2018-10-16)
      Article
      Open Access
      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 ...
    • HyperChromatic trees: a fine-grained approach to distributed algorithms on RedBlack trees 

      Messeguer Peypoch, Xavier; Valles Fuente, Borja (1998-03)
      External research report
      Open Access
      We introduce a relaxed version of RedBlack trees. As concurrent algorithms on balanced search trees are nowadays based on local rules, we propose a set of fine-grained local rules that take more advantage of concurrency ...
    • Long non-coding RNAs as a source of new peptides 

      Ruiz Orera, Jorge; Messeguer Peypoch, Xavier; Subirana Torrent, Juan A.; Albà Soler, M. Mar (2014-09-16)
      Article
      Open Access
      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 ...
    • Massively parallel and distributed dictionaries on AVL and brother trees 

      Gabarró Vallès, Joaquim; Messeguer Peypoch, Xavier (1996-04)
      External research report
      Open Access
      We present a set of local rules to deal with distributed dictionaries, having as a main advantage their possible scheduling in a highly synchronized way to get massively parallel dictionaries on AVLs. Recall that, ...
    • Parallel dictionaries with local rules on AVL and brother trees 

      Messeguer Peypoch, Xavier; Gabarró Vallès, Joaquim (1997-07)
      External research report
      Open Access
      We present a set of local rules to deal with dictionaries, having as a main advantage their possible scheduling in a highly synchronized way to get parallel dictionaries on AVLs. Up to now trees used in massively parallel ...
    • Parallel update and search in skip lists 

      Gabarró Vallès, Joaquim; Martínez Parra, Conrado; Messeguer Peypoch, Xavier (1993-08)
      External research report
      Open Access
      We present a PRAM implementation of a parallel dictionary with skip lists. More precisely, we give algorithms to search, insert and delete k ordered elements in a skip list of n elements in parallel. The algorithms are ...
    • PROMO: detection of transcription regulatory elements using species-tailored searches 

      Albà, Mar; Messeguer Peypoch, Xavier; Escudero, Ruth; Farré, Domènec; Nuñez, Óscar; Martínez, Javier (2002-01)
      External research report
      Open Access
      We have developed a set of tools to construct positional weight matrices from transcription factor binding sites in a species or taxon-specific manner, and to search for matches in DNA sequences. PROMO can be accessed on ...
    • Satellites in the prokaryote world 

      Subirana Torrent, Juan A.; Messeguer Peypoch, Xavier (2019-09-18)
      Article
      Open Access
      Background Satellites or tandem repeats are very abundant in many eukaryotic genomes. Occasionally they have been reported to be present in some prokaryotes, but to our knowledge there is no general comparative study ...
    • Skip trees, an alternative data structure to skip-lists in a concurrent approach 

      Messeguer Peypoch, Xavier (1996-01)
      External research report
      Open Access
      We present a new type of search trees isomorphic to Skip-lists, i.e., there is a one-to-one mapping that commutes with the update algorithms. Moreover, as Skip-trees inherit all the race properties from Skip-lists, they ...
    • Translation of neutrally evolving peptides provides a basis for de novo gene evolution 

      Ruiz Orera, Jorge; Verdaguer Grau, Pol; Villanueva Cañas, José Luis; Messeguer Peypoch, Xavier; Albà Soler, M. Mar (Springer, 2018-03-19)
      Article
      Open Access
      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, ...
    • Where should concurrent rotations take place to rebalance a distributed arbitrary search tree? 

      Bougé, Luc; Gabarró Vallès, Joaquim; Messeguer Peypoch, Xavier (1996-01)
      External research report
      Open Access
      We address the concurrent insertion and deletion of keys in binary almost balanced search trees (AVL trees). We show that this problem can be studied through the self-reorganization of distributed systems of processes ...