Volume 12 Supplement 9

Proceedings of the Ninth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics

Proceedings

Edited by Aaron Darling and Cathal Seoighe

Ninth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics.

Galway, Ireland

8-10 October 2011

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  1. Proceedings

    The rise and fall of breakpoint reuse depending on genome resolution

    During evolution, large-scale genome rearrangements of chromosomes shuffle the order of homologous genome sequences ("synteny blocks") across species. Some years ago, a controversy erupted in genome rearrangem...

    Oliver Attie, Aaron E Darling and Sophia Yancopoulos

    BMC Bioinformatics 2011 12(Suppl 9):S1

    Published on: 5 October 2011

  2. Proceedings

    Evolution of orthologous tandemly arrayed gene clusters

    Tandemly Arrayed Gene (TAG) clusters are groups of paralogous genes that are found adjacent on a chromosome. TAGs represent an important repertoire of genes in eukaryotes. In addition to tandem duplication eve...

    Olivier Tremblay Savard, Denis Bertrand and Nadia El-Mabrouk

    BMC Bioinformatics 2011 12(Suppl 9):S2

    Published on: 5 October 2011

  3. Proceedings

    Fast and accurate methods for phylogenomic analyses

    Species phylogenies are not estimated directly, but rather through phylogenetic analyses of different gene datasets. However, true gene trees can differ from the true species tree (and hence from one another) ...

    Jimmy Yang and Tandy Warnow

    BMC Bioinformatics 2011 12(Suppl 9):S4

    Published on: 5 October 2011

  4. Proceedings

    Fractionation statistics

    Paralog reduction, the loss of duplicate genes after whole genome duplication (WGD) is a pervasive process. Whether this loss proceeds gene by gene or through deletion of multi-gene DNA segments is controversi...

    Baoyong Wang, Chunfang Zheng and David Sankoff

    BMC Bioinformatics 2011 12(Suppl 9):S5

    Published on: 5 October 2011

  5. Proceedings

    Genomic distance under gene substitutions

    The distance between two genomes is often computed by comparing only the common markers between them. Some approaches are also able to deal with non-common markers, allowing the insertion or the deletion of su...

    Marília D V Braga, Raphael Machado, Leonardo C Ribeiro and Jens Stoye

    BMC Bioinformatics 2011 12(Suppl 9):S8

    Published on: 5 October 2011

  6. Proceedings

    The evolution of the tape measure protein: units, duplications and losses

    A large family of viruses that infect bacteria, called phages, is characterized by long tails used to inject DNA into their victims' cells. The tape measure protein got its name because the length of the correspo...

    Mahdi Belcaid, Anne Bergeron and Guylaine Poisson

    BMC Bioinformatics 2011 12(Suppl 9):S10

    Published on: 5 October 2011

  7. Proceedings

    Efficient algorithms for reconstructing gene content by co-evolution

    In a previous study we demonstrated that co-evolutionary information can be utilized for improving the accuracy of ancestral gene content reconstruction. To this end, we defined a new computational problem, th...

    Hadas Birin and Tamir Tuller

    BMC Bioinformatics 2011 12(Suppl 9):S12

    Published on: 5 October 2011

  8. Proceedings

    On the weight of indels in genomic distances

    Classical approaches to compute the genomic distance are usually limited to genomes with the same content, without duplicated markers. However, differences in the gene content are frequently observed and can r...

    Marília D V Braga, Raphael Machado, Leonardo C Ribeiro and Jens Stoye

    BMC Bioinformatics 2011 12(Suppl 9):S13

    Published on: 5 October 2011

  9. Proceedings

    Origin and evolution of gene families in Bacteria and Archaea

    Comparison of complete genomes of Bacteria and Archaea shows that gene content varies considerably and that genomes evolve quite rapidly via gene duplication and deletion and horizontal gene transfer. We analy...

    R Eric Collins, Hugh Merz and Paul G Higgs

    BMC Bioinformatics 2011 12(Suppl 9):S14

    Published on: 5 October 2011

  10. Proceedings

    STELLAR: fast and exact local alignments

    Large-scale comparison of genomic sequences requires reliable tools for the search of local alignments. Practical local aligners are in general fast, but heuristic, and hence sometimes miss significant matches.

    Birte Kehr, David Weese and Knut Reinert

    BMC Bioinformatics 2011 12(Suppl 9):S15

    Published on: 5 October 2011

  11. Proceedings

    Approximating the double-cut-and-join distance between unsigned genomes

    In this paper we study the problem of sorting unsigned genomes by double-cut-and-join operations, where genomes allow a mix of linear and circular chromosomes to be present. First, we formulate an equivalent o...

    Xin Chen, Ruimin Sun and Jiadong Yu

    BMC Bioinformatics 2011 12(Suppl 9):S17

    Published on: 5 October 2011

  12. Proceedings

    Genome dedoubling by DCJ and reversal

    Segmental duplications in genomes have been studied for many years. Recently, several studies have highlighted a biological phenomenon called breakpoint-duplication that apparently associates a significant propor...

    Antoine Thomas, Jean-Stéphane Varré and Aïda Ouangraoua

    BMC Bioinformatics 2011 12(Suppl 9):S20

    Published on: 5 October 2011

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