The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis
Abstract
Genetic sequence alignment is the basis of many evolutionary and comparative studies, and errors in alignments lead to errors in the interpretation of evolutionary information in genomes. Traditional multiple sequence alignment methods disregard the phylogenetic implications of gap patterns that they create and infer systematically biased alignments with excess deletions and substitutions, too few insertions, and implausible insertion-deletion–event histories. We present a method that prevents these systematic errors by recognizing insertions and deletions as distinct evolutionary events. We show theoretically and practically that this improves the quality of sequence alignments and downstream analyses over a wide range of realistic alignment problems. These results suggest that insertions and sequence turnover are more common than is currently thought and challenge the conventional picture of sequence evolution and mechanisms of functional and structural changes.
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Citations
Cites
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Cited by
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An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons
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Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers
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In silico analysis of missense substitutions using sequence-alignment based methods
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Evaluating the Accuracy and Efficiency of Multiple Sequence Alignment Methods
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Jeon, S., Jung, J., Kim, K., Yoo, D., Lee, C., Kang, J., Cho, K., Kang, D.-K., Kwak, W., Yoon, S. H., et al. (2017) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2017.05.015 · Cited by 7
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Detecting Interspecific Positive Selection Using Convolutional Neural Networks
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Self-citation
Metadata
- Authors
- Löytynoja, A., & Goldman, N.
- Venue
- Science
- Published
- 2008-06-20
- Volume
- 320
- Issue
- 5883
- Pages
- 1632-1635
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2017777683
- Cited by
- 802
- References
- 3
- FWCI
- 15.63
- Type
- journal article
- Language
- en
- Open access
- closed
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