http://www.bibsonomy.org/burst/user/dzerbino/Bacterial,BibSonomy BuRST Feed for /user/dzerbino/Bacterial,2008-09-05T08:06:04+02:00http://www.bibsonomy.org/bibtex/217ec918bb871c3d8239479bd26364a71/dzerbinodzerbino2007-09-17T20:19:41+02:00Animals, cerevisiae, Genome, Bacterial, Contig Sequence, Mapping, Sequence Haemophilus Drosophila melanogaster, Software, Consensus Alignment, influenzae, Fungal, Saccharomyces Humans Algorithms, Human, <span style="color:#555555;">Serafim <a href="http://www.bibsonomy.org/author/Batzoglou">Batzoglou</a> und David B <a href="http://www.bibsonomy.org/author/Jaffe">Jaffe</a> und Ken <a href="http://www.bibsonomy.org/author/Stanley">Stanley</a> und Jonathan <a href="http://www.bibsonomy.org/author/Butler">Butler</a> und Sante <a href="http://www.bibsonomy.org/author/Gnerre">Gnerre</a> und Evan <a href="http://www.bibsonomy.org/author/Mauceli">Mauceli</a> und Bonnie <a href="http://www.bibsonomy.org/author/Berger">Berger</a> und Jill P <a href="http://www.bibsonomy.org/author/Mesirov">Mesirov</a> und Eric S <a href="http://www.bibsonomy.org/author/Lander">Lander</a> </span><em>Genome Res</em><em>12(1):177--89</em><em>Jan2002. </em>Mon Sep 17 20:19:41 CEST 2007Genome ResJan1177--89ARACHNE: a whole-genome shotgun assembler122002Animals, cerevisiae, Genome, Bacterial, Contig Sequence, Mapping, Sequence Haemophilus Drosophila melanogaster, Software, Consensus Alignment, influenzae, Fungal, Saccharomyces Humans Algorithms, Human, We describe a new computer system, called ARACHNE, for assembling genome sequence using paired-end whole-genome shotgun reads. ARACHNE has several key features, including an efficient and sensitive procedure for finding read overlaps, a procedure for scoring overlaps that achieves high accuracy by correcting errors before assembly, read merger based on forward-reverse links, and detection of repeat contigs by forward-reverse link inconsistency. To test ARACHNE, we created simulated reads providing approximately 10-fold coverage of the genomes of H. influenzae, S. cerevisiae, and D. melanogaster, as well as human chromosomes 21 and 22. The assemblies of these simulated reads yielded nearly complete coverage of the respective genomes, with a small number of contigs joined into a smaller number of supercontigs (or scaffolds). For example, analysis of the D. melanogaster genome yielded approximately 98% coverage with an N50 contig length of 324 kb and an N50 supercontig length of 5143 kb. The assembly accuracy was high, although not perfect: small errors occurred at a frequency of roughly 1 per 1 Mb (typically, deletion of approximately 1 kb in size), with a very small number of other misassemblies. The assembly was rapid: the Drosophila assembly required only 21 hours on a single 667 MHz processor and used 8.4 Gb of memory.http://www.bibsonomy.org/bibtex/251d90db8174d7d1da830b654951e5ea0/dzerbinodzerbino2007-09-17T20:19:41+02:00Human, Repetitive Contig Nucleic Family Chromosomes, (Genetics), Artificial, Bacterial, Alignment, Algorithms, Cluster Analysis, Biology, Linkage Genome, Sequences, Sequence Mapping, Computational Acid, Multigene Humans, <span style="color:#555555;">Pavel A <a href="http://www.bibsonomy.org/author/Pevzner">Pevzner</a> und Paul A <a href="http://www.bibsonomy.org/author/Pevzner">Pevzner</a> und Haixu <a href="http://www.bibsonomy.org/author/Tang">Tang</a> und Glenn <a href="http://www.bibsonomy.org/author/Tesler">Tesler</a> </span><em>Genome Res</em><em>14(9):1786--96</em><em>Sep2004. </em>Mon Sep 17 20:19:41 CEST 2007Genome ResSep91786--96De novo repeat classification and fragment assembly142004Human, Repetitive Contig Nucleic Family Chromosomes, (Genetics), Artificial, Bacterial, Alignment, Algorithms, Cluster Analysis, Biology, Linkage Genome, Sequences, Sequence Mapping, Computational Acid, Multigene Humans, Repetitive sequences make up a significant fraction of almost any genome, and an important and still open question in bioinformatics is how to represent all repeats in DNA sequences. We propose a new approach to repeat classification that represents all repeats in a genome as a mosaic of sub-repeats. Our key algorithmic idea also leads to new approaches to multiple alignment and fragment assembly. In particular, we show that our FragmentGluer assembler improves on Phrap and ARACHNE in assembly of BACs and bacterial genomes.http://www.bibsonomy.org/bibtex/285853a4fe7db3494508d6631d10f55ca/dzerbinodzerbino2007-09-17T20:19:41+02:00lactis Theoretical, Software, Algorithms, Mapping, Sequence Campylobacter DNA, Bacterial, Neisseria Contig Genome, Models, jejuni, Alignment, meningitidis, Lactococcus Analysis, <span style="color:#555555;">P A <a href="http://www.bibsonomy.org/author/Pevzner">Pevzner</a> und H <a href="http://www.bibsonomy.org/author/Tang">Tang</a> und M S <a href="http://www.bibsonomy.org/author/Waterman">Waterman</a> </span><em>Proc Natl Acad Sci USA</em><em>98(17):9748--53</em><em>Aug2001. </em>Mon Sep 17 20:19:41 CEST 2007Proc Natl Acad Sci USAAug179748--53An Eulerian path approach to DNA fragment assembly982001lactis Theoretical, Software, Algorithms, Mapping, Sequence Campylobacter DNA, Bacterial, Neisseria Contig Genome, Models, jejuni, Alignment, meningitidis, Lactococcus Analysis, For the last 20 years, fragment assembly in DNA sequencing followed the "overlap-layout-consensus" paradigm that is used in all currently available assembly tools. Although this approach proved useful in assembling clones, it faces difficulties in genomic shotgun assembly. We abandon the classical "overlap-layout-consensus" approach in favor of a new euler algorithm that, for the first time, resolves the 20-year-old "repeat problem" in fragment assembly. Our main result is the reduction of the fragment assembly to a variation of the classical Eulerian path problem that allows one to generate accurate solutions of large-scale sequencing problems. euler, in contrast to the celera assembler, does not mask such repeats but uses them instead as a powerful fragment assembly tool.http://www.bibsonomy.org/bibtex/2a94162d90a98876b571cb8460decb1c0/dzerbinodzerbino2007-09-17T20:19:41+02:00Animals, Brucella, Genetic, Bacterial, anthracis Mapping, Dogs, Software Biology, Wolbachia, Validation, Shewanella, Algorithms, Bacillus Staphylococcus, Software, Genomics, Computational Haplotypes, Contig Databases, Benchmarking, Genome, <span style="color:#555555;">Mihai <a href="http://www.bibsonomy.org/author/Pop">Pop</a> und Daniel S <a href="http://www.bibsonomy.org/author/Kosack">Kosack</a> und Steven L <a href="http://www.bibsonomy.org/author/Salzberg">Salzberg</a> </span><em>Genome Res</em><em>14(1):149--59</em><em>Jan2004. </em>Mon Sep 17 20:19:41 CEST 2007Genome ResJan1149--59Hierarchical scaffolding with Bambus142004Animals, Brucella, Genetic, Bacterial, anthracis Mapping, Dogs, Software Biology, Wolbachia, Validation, Shewanella, Algorithms, Bacillus Staphylococcus, Software, Genomics, Computational Haplotypes, Contig Databases, Benchmarking, Genome, The output of a genome assembler generally comprises a collection of contiguous DNA sequences (contigs) whose relative placement along the genome is not defined. A procedure called scaffolding is commonly used to order and orient these contigs using paired read information. This ordering of contigs is an essential step when finishing and analyzing the data from a whole-genome shotgun project. Most recent assemblers include a scaffolding module; however, users have little control over the scaffolding algorithm or the information produced. We thus developed a general-purpose scaffolder, called Bambus, which affords users significant flexibility in controlling the scaffolding parameters. Bambus was used recently to scaffold the low-coverage draft dog genome data. Most significantly, Bambus enables the use of linking data other than that inferred from mate-pair information. For example, the sequence of a completed genome can be used to guide the scaffolding of a related organism. We present several applications of Bambus: support for finishing, comparative genomics, analysis of the haplotype structure of genomes, and scaffolding of a mammalian genome at low coverage. Bambus is available as an open-source package from our Web site.