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Literature DB >> 17895271

CREx: inferring genomic rearrangements based on common intervals.

Matthias Bernt¹, Daniel Merkle, Kai Ramsch, Guido Fritzsch, Marleen Perseke, Detlef Bernhard, Martin Schlegel, Peter F Stadler, Martin Middendorf.

Abstract

SUMMARY: We present the web-based program CREx for heuristically determining pairwise rearrangement events in unichromosomal genomes. CREx considers transpositions, reverse transpositions, reversals and tandem-duplication-random-loss (TDRL) events. It supports the user in finding parsimonious rearrangement scenarios given a phylogenetic hypothesis. CREx is based on common intervals, which reflect genes that appear consecutively in several of the input gene orders. AVAILABILITY: CREx is freely available at http://pacosy.informatik.uni-leipzig.de/crex

Mesh：

Year: 2007 PMID： 17895271 DOI： 10.1093/bioinformatics/btm468

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

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Cited

96 in total

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2. The Entire Mitochondrial Genome of Macrophthalmus abbreviatus Reveals Insights into the Phylogeny and Gene Rearrangements of Brachyura.

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3. Inferring phylogenetic trees from the knowledge of rare evolutionary events.

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4. A comparative study of nemertean complete mitochondrial genomes, including two new ones for Nectonemertes cf. mirabilis and Zygeupolia rubens, may elucidate the fundamental pattern for the phylum Nemertea.

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5. Plastome-Wide Nucleotide Substitution Rates Reveal Accelerated Rates in Papilionoideae and Correlations with Genome Features Across Legume Subfamilies.

Authors: Erika N Schwarz; Tracey A Ruhlman; Mao-Lun Weng; Mohammad A Khiyami; Jamal S M Sabir; Nahid H Hajarah; Njud S Alharbi; Samar O Rabah; Robert K Jansen
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10. Mitochondrial genomes of two Polydora (Spionidae) species provide further evidence that mitochondrial architecture in the Sedentaria (Annelida) is not conserved.

Authors: Lingtong Ye; Tuo Yao; Jie Lu; Jingzhe Jiang; Changming Bai
Journal: Sci Rep Date: 2021-06-30 Impact factor: 4.379

CREx: inferring genomic rearrangements based on common intervals.

1. Comparative analysis of the mitochondrial genomes of Orthonectida: insights into the evolution of an invertebrate parasite species.

2. The Entire Mitochondrial Genome of Macrophthalmus abbreviatus Reveals Insights into the Phylogeny and Gene Rearrangements of Brachyura.

3. Inferring phylogenetic trees from the knowledge of rare evolutionary events.

4. A comparative study of nemertean complete mitochondrial genomes, including two new ones for Nectonemertes cf. mirabilis and Zygeupolia rubens, may elucidate the fundamental pattern for the phylum Nemertea.

5. Plastome-Wide Nucleotide Substitution Rates Reveal Accelerated Rates in Papilionoideae and Correlations with Genome Features Across Legume Subfamilies.

6. A scenario of mitochondrial genome evolution in maize based on rearrangement events.

7. The phylogenetic position of Acoela as revealed by the complete mitochondrial genome of Symsagittifera roscoffensis.

8. Morphological convergence and adaptation in cave and pelagic scale worms (Polynoidae, Annelida).

9. The mitochondrial genomes of the mesozoans Intoshia linei, Dicyema sp. and Dicyema japonicum.

10. Mitochondrial genomes of two Polydora (Spionidae) species provide further evidence that mitochondrial architecture in the Sedentaria (Annelida) is not conserved.