• Mauve

  • Referenced in 15 articles [sw24606]
  • alignment of conserved genomic sequence with rearrangements. As genomes evolve, they undergo large-scale evolutionary ... short sequences. Recombination causes frequent genome rearrangements, horizontal transfer introduces new sequences into bacterial chromosomes ... alignment of conserved genomic DNA in the presence of rearrangements and horizontal transfer. Our methods ... align nine enterobacterial genomes and to determine global rearrangement structure in three mammalian genomes...
  • MSOAR

  • Referenced in 7 articles [sw29658]
  • throughput ortholog assignment system based on genome rearrangement. - MSOAR 2.0: Incorporating tandem duplications into ortholog ... assignment based on genome rearrangement. Background: Ortholog assignment is a critical and fundamental problem ... input genomes in terms of genome rearrangement and gene duplication events. It assumes that ... event inserts a duplicated gene into the genome of interest at a random location...
  • GRIMM

  • Referenced in 5 articles [sw23819]
  • GRIMM: genome rearrangements web server. Genome Rearrangements In Man and Mouse (GRIMM) is a tool ... analyzing rearrangements of gene orders in pairs of unichromosomal and multichromosomal genomes, with either signed ... several programs for analyzing rearrangements in unichromosomal genomes, this is the first to analyze rearrangements...
  • GASTS

  • Referenced in 5 articles [sw29624]
  • GASTS: parsimony scoring under rearrangements. The accumulation of whole-genome data ... renewed interest in the study of genomic rearrangements. Comparative genomics, evolutionary biology, and cancer research ... mechanisms, history, and consequences of these rearrangements. However, rearrangements lead to NP-hard problems ... rearrangement analysis that scales up, in both time and accuracy, to modern high-resolution genomic...
  • Delly

  • Referenced in 3 articles [sw33142]
  • split-read analysis. Motivation: The discovery of genomic structural variants (SVs) at high sensitivity ... understanding pathological somatic rearrangements in personal genome sequencing data. Of particular interest are integrated methods ... split-read alignments to accurately delineate genomic rearrangements at single-nucleotide resolution. DELLY is suitable ... ascertain the full spectrum of genomic rearrangements, including complex events. On simulated data, DELLY compares...
  • CREx

  • Referenced in 4 articles [sw35374]
  • CREx: inferring genomic rearrangements based on common intervals. : We present the web-based program CREx ... heuristically determining pairwise rearrangement events in unichromosomal genomes. CREx considers transpositions, reverse transpositions, reversals ... supports the user in finding parsimonious rearrangement scenarios given a phylogenetic hypothesis. CREx is based...
  • Cgaln

  • Referenced in 2 articles [sw22989]
  • coarse-grained” alignment that can explore genomic rearrangements and reduce the sizes of the regions ... with those of other programs on whole genomic sequences of several bacteria and of some ... also effective in coping with genomic rearrangements. Our results show that Cgaln is very effective...
  • ALF

  • Referenced in 2 articles [sw37905]
  • genome-level aspects such as genome rearrangement and speciation events. Here, we introduce Artificial Life ... range of evolutionary forces that act on genomes: nucleotide, codon, or amino acid substitution (under ... gene loss, gene fusion, gene fission, genome rearrangement, lateral gene transfer (LGT), or speciation...
  • Socrates

  • Referenced in 1 article [sw34368]
  • Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads. Motivation ... Methods for detecting somatic genome rearrangements in tumours using next-generation sequencing are vital ... efficient and effective method for detecting genomic rearrangements in tumours that uses only split-read...
  • Ragout

  • Referenced in 1 article [sw23971]
  • related species/strains. We present Ragout, a genome rearrangement approach, to address this problem. In contrast ... reference-guided algorithms, where only one reference genome is used, Ragout uses multiple references along...
  • CIRCUS

  • Referenced in 1 article [sw23099]
  • sequencing data. Background: Detection of large genomic rearrangements, such as large indels, duplications or translocations ... interpret without an additional visualization step. Circos (Genome Res, 19:1639–1645, 2009), a Perl...
  • MetaSV

  • Referenced in 1 article [sw33140]
  • sequencing. Structural variations (SVs) are large genomic rearrangements that vary significantly in size, making them...
  • deFuse

  • Referenced in 1 article [sw38447]
  • Data. Gene fusions created by somatic genomic rearrangements are known to play an important role...
  • SOPRA

  • Referenced in 8 articles [sw12607]
  • separated by a known distance along the genome. Results: We have developed SOPRA, a tool ... various rearrangement errors. Conclusions: Applying SOPRA to real data from bacterial genomes, we were able...
  • CAR

  • Referenced in 1 article [sw34564]
  • contig assembly of prokaryotic draft genomes using rearrangements. Background: Next generation sequencing technology has allowed...
  • MLGO

  • Referenced in 2 articles [sw29621]
  • data. Background: The rapid accumulation of whole-genome data has renewed interest in the study ... support duplication and loss events along with rearrangements. Results: MLGO (Maximum Likelihood for Gene-Order ... reconstruction of phylogeny and/or ancestral genomes from gene-order data. MLGO is based on likelihood ... analysis of large-scale genomic changes including not only rearrangements but also gene insertions, deletions...
  • PennCNV

  • Referenced in 16 articles [sw19390]
  • resolution copy number variation detection in whole-genome SNP genotyping data. Comprehensive identification and cataloging ... median size of ∼12 kb. Excluding common rearrangements in lymphoblastoid cell lines, the fraction ... results demonstrate the feasibility of whole-genome fine-mapping of CNVs via high-density...
  • MAPIT

  • Referenced in 1 article [sw17259]
  • gene content and organization, genome information density and rearrangements, as well as comparison of genome...
  • Mugsy

  • Referenced in 4 articles [sw16994]
  • align mixtures of assembled draft and completed genome data, and is robust in identifying ... rich complement of genetic variation including duplications, rearrangements, and large-scale gain and loss...
  • GRAPPA

  • Referenced in 12 articles [sw17255]
  • gene rearrangements. Phylogenetic reconstruction from gene rearrangements has attracted increasing attention from biologists and computer ... approach, but has been limited to small genomes because the running time of its scoring...