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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, Ireland8-10 October 2011

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  1. Content type: Proceedings

    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...

    Authors: Oliver Attie, Aaron E Darling and Sophia Yancopoulos

    Citation: BMC Bioinformatics 2011 12(Suppl 9):S1

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  2. Content type: Proceedings

    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...

    Authors: Olivier Tremblay Savard, Denis Bertrand and Nadia El-Mabrouk

    Citation: BMC Bioinformatics 2011 12(Suppl 9):S2

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  3. Content type: Proceedings

    The lengths of 5’UTRs of multicellular eukaryotes have been suggested to be subject to stochastic changes, with upstream start codons (uAUGs) as the major constraint to suppress 5’UTR elongation. However, this...

    Authors: Chun-Hsi Chen, Hsuan-Yu Lin, Chia-Lin Pan and Feng-Chi Chen

    Citation: BMC Bioinformatics 2011 12(Suppl 9):S3

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  4. Content type: Proceedings

    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) ...

    Authors: Jimmy Yang and Tandy Warnow

    Citation: BMC Bioinformatics 2011 12(Suppl 9):S4

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  5. Content type: Proceedings

    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...

    Authors: Baoyong Wang, Chunfang Zheng and David Sankoff

    Citation: BMC Bioinformatics 2011 12(Suppl 9):S5

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  6. Content type: Proceedings

    A gene tree for a gene family is often discordant with the containing species tree because of its complex evolutionary course during which gene duplication, gene loss and incomplete lineage sorting events migh...

    Authors: Taoyang Wu and Louxin Zhang

    Citation: BMC Bioinformatics 2011 12(Suppl 9):S7

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  7. Content type: Proceedings

    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...

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

    Citation: BMC Bioinformatics 2011 12(Suppl 9):S8

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  8. Content type: Proceedings

    The identification of functional regions contained in a given multiple sequence alignment constitutes one of the major challenges of comparative genomics. Several studies have focused on the identification of ...

    Authors: Dunarel Badescu, Alix Boc, Abdoulaye Baniré Diallo and Vladimir Makarenkov

    Citation: BMC Bioinformatics 2011 12(Suppl 9):S9

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  9. Content type: Proceedings

    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...

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

    Citation: BMC Bioinformatics 2011 12(Suppl 9):S13

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  10. Content type: Proceedings

    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...

    Authors: R Eric Collins, Hugh Merz and Paul G Higgs

    Citation: BMC Bioinformatics 2011 12(Suppl 9):S14

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  11. Content type: Proceedings

    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.

    Authors: Birte Kehr, David Weese and Knut Reinert

    Citation: BMC Bioinformatics 2011 12(Suppl 9):S15

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  12. Content type: Proceedings

    Changes in transcriptional orientation (“CTOs”) occur frequently in prokaryotic genomes. Such changes usually result from genomic inversions, which may cause a conflict between the directions of replication an...

    Authors: Chieh-Hua Lin, Chun-Yi Lian, Chao Agnes Hsiung and Feng-Chi Chen

    Citation: BMC Bioinformatics 2011 12(Suppl 9):S19

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  13. Content type: Proceedings

    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...

    Authors: Antoine Thomas, Jean-Stéphane Varré and Aïda Ouangraoua

    Citation: BMC Bioinformatics 2011 12(Suppl 9):S20

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