BMC Bioinformatics BioMed Central Methodology article SynBlast: Assisting the analysis of conserved synteny information

[1]  Erik L. L. Sonnhammer,et al.  InParanoid 6: eukaryotic ortholog clusters with inparalogs , 2007, Nucleic Acids Res..

[2]  Andreas Prlic,et al.  Ensembl 2008 , 2007, Nucleic Acids Res..

[3]  Evgeny M. Zdobnov,et al.  OrthoDB: the hierarchical catalog of eukaryotic orthologs , 2007, Nucleic Acids Res..

[4]  Sonja J. Prohaska,et al.  The duplication of the Hox gene clusters in teleost fishes , 2004, Theory in Biosciences.

[5]  Jos Boekhorst,et al.  Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties , 2007, BMC Bioinformatics.

[6]  Axel Meyer,et al.  Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni , 2007, BMC Genomics.

[7]  David Sankoff,et al.  Algorithms for the Extraction of Synteny Blocks from Comparative Maps , 2007, WABI.

[8]  A. Meyer,et al.  Comparative genomics of ParaHox clusters of teleost fishes: gene cluster breakup and the retention of gene sets following whole genome duplications , 2007, BMC Genomics.

[9]  Denis Duboule,et al.  The rise and fall of Hox gene clusters , 2007, Development.

[10]  K. Howe,et al.  Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. , 2007, Genome research.

[11]  Sonja J. Prohaska,et al.  Evolution of the vertebrate ParaHox clusters. , 2006, Journal of experimental zoology. Part B, Molecular and developmental evolution.

[12]  Leo Goodstadt,et al.  Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human , 2006, PLoS Comput. Biol..

[13]  C. Soderlund,et al.  SyMAP: A system for discovering and viewing syntenic regions of FPC maps. , 2006, Genome research.

[14]  P. Holland,et al.  Breakup of a homeobox cluster after genome duplication in teleosts , 2006, Proceedings of the National Academy of Sciences.

[15]  Laurent Duret,et al.  The Xist RNA Gene Evolved in Eutherians by Pseudogenization of a Protein-Coding Gene , 2006, Science.

[16]  A. Durston,et al.  The zebrafish hoxDb cluster has been reduced to a single microRNA , 2006, Nature Genetics.

[17]  Peter F Stadler,et al.  The "fish-specific" Hox cluster duplication is coincident with the origin of teleosts. , 2006, Molecular biology and evolution.

[18]  Bernard B. Suh,et al.  Reconstructing contiguous regions of an ancestral genome. , 2006, Genome research.

[19]  Jordi Garcia-Fernàndez,et al.  The genesis and evolution of homeobox gene clusters , 2005, Nature Reviews Genetics.

[20]  B. Venkatesh,et al.  A Genetic Linkage Map for the Tiger Pufferfish, Takifugu rubripes , 2005, Genetics.

[21]  Axel Meyer,et al.  Hox clusters as models for vertebrate genome evolution. , 2005, Trends in genetics : TIG.

[22]  Richard J. Mural,et al.  Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs , 2005, Bioinform..

[23]  Erik L. L. Sonnhammer,et al.  Inparanoid: a comprehensive database of eukaryotic orthologs , 2004, Nucleic Acids Res..

[24]  Sonja J. Prohaska,et al.  Molecular Evolution of Duplicated Ray Finned Fish HoxA Clusters: Increased Synonymous Substitution Rate and Asymmetrical Co-divergence of Coding and Non-coding Sequences , 2005, Journal of Molecular Evolution.

[25]  Steven Salzberg,et al.  DAGchainer: a tool for mining segmental genome duplications and synteny , 2004, Bioinform..

[26]  M. Nóbrega,et al.  Comparative genomics at the vertebrate extremes , 2004, Nature Reviews Genetics.

[27]  Sonja J. Prohaska,et al.  The Footprint Sorting Problem , 2004, J. Chem. Inf. Model..

[28]  Angel Amores,et al.  Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish. , 2003, Genome research.

[29]  Bonnie Berger,et al.  Whole-genome comparative annotation and regulatory motif discovery in multiple yeast species , 2003, RECOMB '03.

[30]  David Sankoff,et al.  The Reconstruction of Doubled Genomes , 2003, SIAM J. Comput..

[31]  A. Meyer,et al.  Genome duplication, a trait shared by 22000 species of ray-finned fish. , 2003, Genome research.

[32]  P. Pevzner,et al.  Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. , 2003, Genome research.

[33]  J. Raes,et al.  The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. , 2002, Genome research.

[34]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[35]  Christian E. V. Storm,et al.  Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. , 2001, Journal of molecular biology.

[36]  P. Holland.  Beyond the Hox: how widespread is homeobox gene clustering? , 2001, Journal of anatomy.

[37]  Peter W. H. Holland,et al.  Ancient origin of the Hox gene cluster , 2001, Nature Reviews Genetics.

[38]  E. Stellwag,et al.  Hox gene duplication in fish. , 1999, Seminars in cell & developmental biology.

[39]  G. Wagner,et al.  Phylogenetic reconstruction of vertebrate Hox cluster duplications. , 1997, Molecular biology and evolution.

[40]  Gapped BLAST and PSI-BLAST: A new , 1997 .

[41]  William McGinnis,et al.  Homeobox genes and axial patterning , 1992, Cell.

[42]  D. Duboule,et al.  The structural and functional organization of the murine HOX gene family resembles that of Drosophila homeotic genes. , 1989, The EMBO journal.