{"id":1886,"date":"2013-10-10T09:50:59","date_gmt":"2013-10-10T01:50:59","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=1886"},"modified":"2013-10-10T10:58:14","modified_gmt":"2013-10-10T02:58:14","slug":"%e6%af%94%e8%be%83%e5%9f%ba%e5%9b%a0%e7%bb%84%e7%bb%84%e8%a3%85%ef%bc%88comparative-genome-assembly%ef%bc%89","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=1886","title":{"rendered":"Methods of comparative genome assembly"},"content":{"rendered":"

\u540c\u4e00\u7269\u79cd\u5f97\u5230\u4e86\u591a\u4e2a\u57fa\u56e0\u7ec4\u7ec4\u88c5\u7ed3\u679c\uff0c\u5982\u4f55\u5c06\u7ec4\u88c5\u7ed3\u679c\u8fdb\u884c\u5408\u5e76\uff0c\u4ece\u800c\u4f7f\u57fa\u56e0\u7ec4\u66f4\u5b8c\u6574\uff1f
\nParrish N, Sudakov B, Eskin E. Genome reassembly with high-throughput sequencing data[J]. BMC genomics, 2013, 14(Suppl 1): S8.<\/a>\u4e00\u6587\u4e2d\u63d0\u5230\uff1a
\nA number of software packages have been developed in recent years with the aim of utilizing a set of reference genomes to produce a more optimized scaffolding, or layout, of the contigs produced in de novo assembly. OSLay [20] uses a maximum-weight matching algorithm to identify likely neighboring contigs. Treecat [21] builds a fully connected graph of the contigs, with edges weighted by the distance between syntenic regions in the reference, and attempts to find a minimum-weight Hamiltonian path through the graph using a greedy heuristic. Finally, PGA [22] uses a genetic algorithm to search the space of possible contig orderings. By relying on the contigs produced through de novo assembly, however, these methods may not take full advantage of the reference genome.
\n\u4ece\u8be5\u7bc7\u6587\u7ae0\u5f00\u59cb\uff0c\u5bfb\u627e\u65b9\u6cd5\uff1a<\/p>\n

1. AMOScmp<\/h1>\n

\u5f15\u7528\u6587\u732e\uff1aPop M, Phillippy A, Delcher A L, et al. Comparative genome assembly[J]. Briefings in bioinformatics, 2004, 5(3): 237-248.<\/a><\/p>\n

AMOScmp applies a modified MUMmer algorithm to a newly sequenced genome by mapping it onto a reference genome.<\/p>\n

Hawkeye and AMOS are available open source at http:\/\/amos.sourceforge.net<\/a>. <\/p>\n

2. Projector 2<\/h1>\n

\u5f15\u7528\u6587\u732e\uff1avan Hijum S A F T, Zomer A L, Kuipers O P, et al. Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies[J]. Nucleic acids research, 2005, 33(suppl 2): W560-W566.<\/a><\/p>\n

\u6587\u7ae0\u4e2d\u5199\u9053\uff1a
\nProjector 2 has several distinctive features: a user-friendly web interface, automatic removal of repetitive elements (repeat-masking) and automated primer design for gap-closure purposes. The web interface is freely accessible at http:\/\/molgen.biol.rug.nl\/websoftware\/projector2<\/a>. <\/p>\n

3. OSLay<\/h1>\n

\u5f15\u7528\u6587\u732e\uff1aRichter D C, Schuster S C, Huson D H. OSLay: optimal syntenic layout of unfinished assemblies[J]. Bioinformatics, 2007, 23(13): 1573-1579.<\/a><\/p>\n

\u8be5\u6587\u7ae0\u4e2d\u5199\u9053\uff1a
\nThe underlying algorithm is based on maximum weight matching. The tool provides an interactive visualization of the computed layout and the result can be imported into the assembly editing tool Consed to support the design of primer pairs for gap closure. <\/p>\n

OSLay is freely available from: http:\/\/www-ab.informatik.unituebingen.de\/software\/oslay<\/a><\/p>\n

4. PGA<\/h1>\n

\u5f15\u7528\u6587\u732e\uff1aZhao F, Zhao F, Li T, et al. A new pheromone trail-based genetic algorithm for comparative genome assembly[J]. Nucleic acids research, 2008, 36(10): 3455-3462.<\/a><\/p>\n

\u8be5\u6587\u7ae0\u4e2d\u5199\u9053\uff1a
\nA pheromone trail-based genetic algorithm (PGA) was used to search globally for the optimal placement for each contig.An extended version of PGA can predict additional candidate connections for each contig and can thus increase the likelihood of identifying the correct arrangement of each contig. The software and test data sets can be accessed at http:\/\/sourceforge.net\/projects\/pga4genomics\/<\/a>. <\/p>\n

5.Treecat<\/h1>\n

\u5f15\u7528\u6587\u732e\uff1aHusemann P, Stoye J. Phylogenetic comparative assembly[J]. Algorithms for Molecular Biology, 2010, 5(3).<\/a><\/p>\n

\u8be5\u6587\u7ae0\u4e2d\u5199\u9053\uff1a
\nOur new algorithm for contig ordering uses sequence similarity as well as phylogenetic information to estimate adjacencies of contigs. An evaluation of our implementation shows that it performs better than recent approaches while being much faster at the same time.
\nThe software is open source (GPL) and available within the Comparative Genomics – Contig Arrangement Toolsuite (cg-cat, http:\/\/bibiserv.techfak.uni-bielefeld.de\/cg-cat<\/a> webcite) on the Bielefeld Bioinformatics Server (BiBiServ).<\/p>\n","protected":false},"excerpt":{"rendered":"

\u540c\u4e00\u7269\u79cd\u5f97\u5230\u4e86\u591a\u4e2a\u57fa\u56e0\u7ec4\u7ec4\u88c5\u7ed3\u679c\uff0c\u5982\u4f55\u5c06\u7ec4\u88c5\u7ed3\u679c\u8fdb\u884c\u5408\u5e76\uff0c\u4ece\u800c\u4f7f\u57fa\u56e0\u7ec4\u66f4\u5b8c\u6574\uff1f … \u7ee7\u7eed\u9605\u8bfb →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[3],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1886"}],"collection":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=1886"}],"version-history":[{"count":15,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1886\/revisions"}],"predecessor-version":[{"id":1901,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1886\/revisions\/1901"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1886"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1886"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1886"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}