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JCoast - A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes

by: Michael Richter, Thierry Lombardot, Ivaylo Kostadinov, Renzo Kottmann, Melissa B. Duhaime, Jorg Peplies, Frank O. Glockner

BMC Bioinformatics, Vol. 9 (01 April 2008), 177.

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1998 2002 2005 2006 2007 2008 454 abitalk abruijn abundance accuracy acinetobacters adaptation adaptive aerobes algorithm algorithms aligment alignment alignment-accuracy alignment-free alignments alignmnent allelic alternative-splicing amino-acid amplification analyses analysis ancestral annealing annotation antibiotic approximate archaea archael arrangements assembly astrocyte astrocytes bacillus bacteria bacterial bayesian bbh bias bibliographic-tools bioinformatics biology biomoby blast book browser burkholderia case-study caspase caspase-3 chromosome chromsome circular classification closely-related closely-relted clustal clustering clusters coalescent codon-usage collinear communities comparative-genomics comparison compiler compoosition composition compressed compression concatenated concatenation consensus conservartion convergence core corealigner core-genome crispr cyano damage database decay deleterious denovo detection development dialign diet digital dinucleotide disorder distance divergence diverisity diversity dna dna-repeats dna-replication dna-sequences dnds drosophila duplication dupvshgt dus dynamic ecoli editor edsi elements email ensembl error escitotoxicity essential-genes eukaryote eurkaryote evalue evolution evolutionary exact excitotoxic expert-systems families fasta fate francisella fw gamma gap gap-open gapped gapped-seeds gap-penalty gaps gc gene gene-content gene-conversion gene-dosage gene-duplication gene-evolution gene-flux gene-genesis gene-loss gene-order gene-phylogeny genes genetic gene-transfer gene-tree genome genome-aligment genome-alignment genome-comparison genome-evolution genome-organization genome-phylogeny genome-rearrangement genome-sequence genome-taxonomy genomic-era genomic-islands genomics geometry gibbs glia greedy grid gut hash hgt hitch-hiking hmm homologous homologous-recombination homology homology-map hops hot hsp human human-mouse hypermutabiliy incomplete incongruence indel-rates indels infection inference influenzae insertion-sequences interactive interface ischemia jctalk jctalk2 kmer-frequencies ktuple language large-scale lca library likelihood linear lma local local-alignment loci logo mammals mammoth markov-model matbal matches match-filtration matrix maximal maximum maximum-likelihood mcl mcmc mems metagenome metagenomics method mga microbiota microcystis minimum model monte-carlo motif motility msa multiple mummer muscle mutation mutational mutations mutualism mycoplasma natural nautila neisseria neonatal network networking networks neurons neutrality niche noncoding novel-genes nralign nucleotide o127h6 oligonucleotide online operon optimization organization organs orientia origin ortholog orthologs oxygen pairwise pan-genome paralog parameters parametric parasitism parsimony pathogen pathogens pathways pecan pectobacterium phage pharmacogenomic phlogenetic phmm phylgenomics phylogenetic phylogenetics phylogenomic phylogenomics phylogeny pipeline plant plasticity poa poisson population population-genetics population-size positive posterior probabilities profundicola programming progressive prokaryote prokaryotic protein protein-repeats proteins proteome proteomes pseudogene pseudogenes pseudomonas pvalue quality r randomwalks rapidly-evolving rare rat rearangements rearrangements recombination reconstruction reduction refinement regulatory reliability repeat repeat-families repeats repeatscout repetitiveness replication resistance resource review rickettsia rrna salmonella scientific score scoring scoring-schemes segment segmental segment-based selection sequence sequence-alignment sequence-assembly sequences sequencing set sex shigella significance sim2 similarity simulating-evolution simulation softwaare software sp speciation species species-phylogeny splitstree ssr statistical statistical-alignment statistics string structural-repeats structure study submarine subsitution substitution substitution-rate substring suffix survivin svs sybmionts synonymous synteny synthetic tandem-duplication technology testing tol transposable transposable-elements transpositions tree trees ultraconserved ungapped ungapped-alignment vertebrates vibrio virulence virus visualization wabi08 webserver wgc whole-genome why-published-research-findings-are-false wolbachia wooly word xanthomonadales xplorseq yang yin

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