SMORE: Synteny Modulator of Repetitive Elements
Abstract
:1. Introduction
2. Methods
2.1. Overview
2.2. Annotation of the Loci of Interest
2.3. Genomic Anchors
- For the genetic element , we can find two flanking regions and that have orthologous counterparts and in species B on the basis of sequence similarity.
- On the basis of genomic coordinates, the order of the sequences is determined such that and .
2.4. Candidate Clusters of Co-Orthologous Genes
- The relative genomic order of the elements in each cluster is the same.
- There are no elements belonging to another cluster between the the elements of and .
- The total extension of the merge cluster does not exceed a user-defined threshold.
2.4.1. Counting Events Using Relaxed Adjacency Conditions
2.4.2. Orthologs
2.5. Quantitative Analysis of Evolutionary Events
2.6. Pseudogenes and Remolding Events
2.7. Implementation
- A MSA of the genomes under consideration is required to extract the synteny anchor points. Currently only Multiz format is supported.
- The corresponding genomic sequences are required for the annotation of the loci of interest. The pipeline expects fasta format. Because there is no guarantee that genome-wide MSA represents the complete genome, both MSA and genomes must be provided.
- Target elements can be specified either as user-supplied annotation files or as one or more covariance models for annotation with Infernal or tRNAscan-SE. The modular organization of the pipeline makes it straightforward to add, in future releases, further means of generating annotation information, such as hidden Markov models of proteins.
- A phylogenetic tree of the species of interest is necessary as a background to which evolutionary events are mapped.
2.8. Benchmarking with Artifical Data
3. Results
3.1. Automatic Pipeline for Multicopy Elements
3.2. Application to Artificial Data
3.3. tRNAs
3.4. Mammalian Y RNAs
3.5. Nematode stem-bulge RNAs
4. Discussion and Concluding Remarks
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Berkemer, S.J.; Hoffmann, A.; Murray, C.R.A.; Stadler, P.F. SMORE: Synteny Modulator of Repetitive Elements. Life 2017, 7, 42. https://doi.org/10.3390/life7040042
Berkemer SJ, Hoffmann A, Murray CRA, Stadler PF. SMORE: Synteny Modulator of Repetitive Elements. Life. 2017; 7(4):42. https://doi.org/10.3390/life7040042
Chicago/Turabian StyleBerkemer, Sarah J., Anne Hoffmann, Cameron R. A. Murray, and Peter F. Stadler. 2017. "SMORE: Synteny Modulator of Repetitive Elements" Life 7, no. 4: 42. https://doi.org/10.3390/life7040042