Barcodes for genomes and applications Export

@article{Zhou2008, abstract = {BACKGROUND:Each genome has a stable distribution of the combined frequency for each k-mer and its reverse complement measured in sequence fragments as short as 1000 bps across the whole genome, for 1<k<6. The collection of these k-mer frequency distributions is unique to each genome and termed the genome's barcode.RESULTS:We found that for each genome, the majority of its short sequence fragments have highly similar barcodes while sequence fragments with different barcodes typically correspond to genes that are horizontally transferred or highly expressed. This observation has led to new and more effective ways for solving two challenging problems: metagenome binning problem and identification of horizontally transferred genes. Our barcode-based metagenome binning algorithm substantially improves the state of the art in terms of both binning accuracies and the scope of applicability. Other attractive properties of genomes barcodes include (a) the barcodes have different and identifiable characteristics for different classes of genomes like prokaryotes, eukaryotes, mitochondria and plastids, and (b) barcodes similarities are generally proportional to the genomes' phylogenetic closeness. CONCLUSIONS:These and other properties of genomes barcodes make them a new and powerful tool for studying numerous genome and metagenome analysis problems.}, author = {Zhou, Fengfeng and Olman, Victor and Xu, Ying}, citeulike-article-id = {3803143}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2105-9-546}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19091119}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19091119}, doi = {10.1186/1471-2105-9-546}, issn = {1471-2105}, journal = {BMC Bioinformatics}, keywords = {e\_coli, electrostatics}, number = {1}, posted-at = {2009-01-07 17:36:12}, priority = {2}, title = {Barcodes for genomes and applications}, url = {http://dx.doi.org/10.1186/1471-2105-9-546}, volume = {9}, year = {2008} }

TY - JOUR ID - Zhou2008 L3 - citeulike-article-id:3803143 N2 - BACKGROUND:Each genome has a stable distribution of the combined frequency for each k-mer and its reverse complement measured in sequence fragments as short as 1000 bps across the whole genome, for 1<k<6. The collection of these k-mer frequency distributions is unique to each genome and termed the genome's barcode.RESULTS:We found that for each genome, the majority of its short sequence fragments have highly similar barcodes while sequence fragments with different barcodes typically correspond to genes that are horizontally transferred or highly expressed. This observation has led to new and more effective ways for solving two challenging problems: metagenome binning problem and identification of horizontally transferred genes. Our barcode-based metagenome binning algorithm substantially improves the state of the art in terms of both binning accuracies and the scope of applicability. Other attractive properties of genomes barcodes include (a) the barcodes have different and identifiable characteristics for different classes of genomes like prokaryotes, eukaryotes, mitochondria and plastids, and (b) barcodes similarities are generally proportional to the genomes' phylogenetic closeness. CONCLUSIONS:These and other properties of genomes barcodes make them a new and powerful tool for studying numerous genome and metagenome analysis problems. IS - 1 JF - BMC Bioinformatics SN - 1471-2105 TI - Barcodes for genomes and applications VL - 9 KW - e_coli KW - electrostatics AU - Zhou, Fengfeng AU - Olman, Victor AU - Xu, Ying PY - 2008/// UR - http://dx.doi.org/10.1186/1471-2105-9-546 ER -