2008-3-mdb 454 accuracy alignment alternative alu annotation apobec arabidopsis bacteria bayesian breakpoints chimera chip-on-chip chip-seq cis-regulation cis-regulatory cns-differences cns-ranking coding codon_bias codon_usage collaboratories comparative_genomics comparison conserved core_promoter cost da database defragmentation dna dna_structure domestication drosophila ecoli editing enzyme epigenetics erv est evolution evolutionary-rate exon exonisation expression families fixation flies flux-balance-analysis fungi gene gene-duplication gene_order genes genome genome_browser genome-scale-models genome_sequence hmm human inhibition insertion intron introns l1 light-shotgun line ltr mammal mammals matrix microarray mirna model motif motif-discovery networks new noncoding opinion overlapping_gene pelement p-element plants positiveselection primer promoter protein-coding pyrosequencing r rate_of_evolution rearrangement regulation retroelement review rice rna rna_editing roc semantic_web sequence sites snp snrna software splice splicing standards statistics target te text_mining tfbs tissue tool transcription transposable-element transposon tss tutorial u7 utr variation vertebrate visualization worms xiao yeast