FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W4213305707> ?p ?o ?g. }

• W4213305707 abstract "A bstract Phylogenetic inference based on genomic structural variations, that manipulate the gene order and content of whole chromosomes, promises to inform a more comprehensive understanding of evolution. The first challenge in using such data, the incompleteness of available de novo assemblies, is easing as long read technologies enable (near-)complete genome assembly, but methodological challenges remain. To obtain the input to rearrangement-based inference methods, we need to detect syntenic blocks of orthologous sequences, a task that can be accomplished in many ways, none of which are obviously preferable. In this paper, we use 94 reference quality genomes of primarily Mycobacterium tuberculosis (Mtb) isolates as a benchmark to evaluate these methods. The clonal nature of Mtb evolution, the manageable genome sizes, along with substantial levels of structural variation make this an ideal benchmarking dataset. We test several methods for detecting homology and obtaining syntenic blocks, and two methods for inferring phylogenies, comparing them to the standard method that uses substitutions for inferring the tree. We find that not only the choice of methods but also their parameters can impact results, especially among branches with lower support. In particular, a method based on an encoding of adjacencies applied to Cactus-defined blocks was fully compatible with the highly supported branches of the substitution-based tree. Thus, we were able to combine the two trees to obtain a supertree with high resolution utilizing both SNPs and rearrangements. Furthermore, we observed that the results were much less affected by the choice of the tree inference method than by the method used to determine the underlying syntenic blocks. Overall, our results indicate that accurate trees can be inferred using genome rearrangements, but the choice of the methods for inferring the homology matters and requires care." @default.
• W4213305707 created "2022-02-24" @default.
• W4213305707 creator A5014999428 @default.
• W4213305707 creator A5025159794 @default.
• W4213305707 creator A5042304681 @default.
• W4213305707 creator A5087959579 @default.
• W4213305707 date "2022-02-19" @default.
• W4213305707 modified "2023-10-12" @default.
• W4213305707 title "Evaluating Impacts of Syntenic Block Detection Strategies on Rearrangement Phylogeny Using M. tuberculosis Isolates" @default.
• W4213305707 cites W1968206926 @default.
• W4213305707 cites W1982579644 @default.
• W4213305707 cites W1983403167 @default.
• W4213305707 cites W1986009232 @default.
• W4213305707 cites W1997631042 @default.
• W4213305707 cites W2002833133 @default.
• W4213305707 cites W2007668764 @default.
• W4213305707 cites W2014270275 @default.
• W4213305707 cites W2015498428 @default.
• W4213305707 cites W2019829411 @default.
• W4213305707 cites W2026452889 @default.
• W4213305707 cites W2031366058 @default.
• W4213305707 cites W2035525755 @default.
• W4213305707 cites W2049796549 @default.
• W4213305707 cites W2058417246 @default.
• W4213305707 cites W2060425093 @default.
• W4213305707 cites W206494857 @default.
• W4213305707 cites W2067117360 @default.
• W4213305707 cites W2070018389 @default.
• W4213305707 cites W2075111823 @default.
• W4213305707 cites W2090002702 @default.
• W4213305707 cites W2090392412 @default.
• W4213305707 cites W2094720766 @default.
• W4213305707 cites W2096093282 @default.
• W4213305707 cites W2102619694 @default.
• W4213305707 cites W2102692786 @default.
• W4213305707 cites W2103673802 @default.
• W4213305707 cites W2107282968 @default.
• W4213305707 cites W2110560983 @default.
• W4213305707 cites W2113265821 @default.
• W4213305707 cites W2113317197 @default.
• W4213305707 cites W2124166542 @default.
• W4213305707 cites W2124321327 @default.
• W4213305707 cites W2126423997 @default.
• W4213305707 cites W2127639177 @default.
• W4213305707 cites W2127860913 @default.
• W4213305707 cites W2130206397 @default.
• W4213305707 cites W2132972885 @default.
• W4213305707 cites W2139736670 @default.
• W4213305707 cites W2141052558 @default.
• W4213305707 cites W2141274012 @default.
• W4213305707 cites W2141581393 @default.
• W4213305707 cites W2151009141 @default.
• W4213305707 cites W2155865869 @default.
• W4213305707 cites W2156125289 @default.
• W4213305707 cites W2160025165 @default.
• W4213305707 cites W2161973008 @default.
• W4213305707 cites W2162055898 @default.
• W4213305707 cites W2170747616 @default.
• W4213305707 cites W2171231095 @default.
• W4213305707 cites W2202810729 @default.
• W4213305707 cites W2293111751 @default.
• W4213305707 cites W2501571505 @default.
• W4213305707 cites W2513727910 @default.
• W4213305707 cites W2590646912 @default.
• W4213305707 cites W2611920982 @default.
• W4213305707 cites W2733127495 @default.
• W4213305707 cites W2765298478 @default.
• W4213305707 cites W2769447976 @default.
• W4213305707 cites W2771760123 @default.
• W4213305707 cites W2788327314 @default.
• W4213305707 cites W2802044770 @default.
• W4213305707 cites W2899025479 @default.
• W4213305707 cites W2899036110 @default.
• W4213305707 cites W2944768395 @default.
• W4213305707 cites W2947780575 @default.
• W4213305707 cites W2950150251 @default.
• W4213305707 cites W2950354111 @default.
• W4213305707 cites W2952386282 @default.
• W4213305707 cites W2952463453 @default.
• W4213305707 cites W2953328352 @default.
• W4213305707 cites W2967476242 @default.
• W4213305707 cites W2977811825 @default.
• W4213305707 cites W2994814458 @default.
• W4213305707 cites W3093976573 @default.
• W4213305707 cites W3100651612 @default.
• W4213305707 cites W3111607156 @default.
• W4213305707 cites W3120798773 @default.
• W4213305707 cites W3127314690 @default.
• W4213305707 cites W3143333549 @default.
• W4213305707 cites W3159728495 @default.
• W4213305707 cites W3163990482 @default.
• W4213305707 cites W4250164480 @default.
• W4213305707 doi "https://doi.org/10.1101/2022.02.18.481113" @default.
• W4213305707 hasPublicationYear "2022" @default.
• W4213305707 type Work @default.
• W4213305707 citedByCount "1" @default.
• W4213305707 countsByYear W42133057072022 @default.
• W4213305707 crossrefType "posted-content" @default.
• W4213305707 hasAuthorship W4213305707A5014999428 @default.
• W4213305707 hasAuthorship W4213305707A5025159794 @default.

• next