ArticleNucleic acids research2014
Improved search heuristics find 20,000 new alignments between human and mouse genomes.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed.
- KegAlign: optimizing pairwise alignments with diagonal partitioning.Genome biology · 2025Article
- Article
- Convergent genomic signatures associated with vertebrate viviparity.BMC biology · 2024Article
- DomesticatingFrontiers in plant science · 2023Article
- Global, highly specific and fast filtering of alignment seeds.BMC bioinformatics · 2022Article
- A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants.The plant genome · 2022Article
- Paleozoic Protein Fossils Illuminate the Evolution of Vertebrate Genomes and Transposable Elements.Molecular biology and evolution · 2022Article
- De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes.Science (New York, N.Y.) · 2021Article
- Genomic insights into the host specific adaptation of the Pneumocystis genus.Communications biology · 2021Article
- lncEvo: automated identification and conservation study of long noncoding RNAs.BMC bioinformatics · 2021Article
- Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion.BMC biology · 2020Article
- Adaptive Strategies of the Candidate Probiotic E. coli Nissle in the Mammalian Gut.Cell host & microbe · 2019Article
- A genome-wide survey with different rapeseed ecotypes uncovers footprints of domestication and breeding.Journal of experimental botany · 2017Article
- A simple and economical method for improving whole genome alignment.BMC genomics · 2017Article
- Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds.Algorithms for molecular biology : AMB · 2017Article
- rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison.PLoS computational biology · 2016Article
- Split-alignment of genomes finds orthologies more accurately.Genome biology · 2015Article
- A coverage criterion for spaced seeds and its applications to support vector machine string kernels and k-mer distances.Journal of computational biology : a journal of computational molecular cell biology · 2014Article
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2 authors.
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Abstract
Sequence similarity search is a fundamental way of analyzing nucleotide sequences. Despite decades of research, this is not a solved problem because there exist many similarities that are not found by current methods. Search methods are typically based on a seed-and-extend approach, which has many variants (e.g. spaced seeds, transition seeds), and it remains unclear how to optimize this approach. This study designs and tests seeding methods for inter-mammal and inter-insect genome comparison. By considering substitution patterns of real genomes, we design sets of multiple complementary transition seeds, which have better performance (sensitivity per run time) than previous seeding strategies. Often the best seed patterns have more transition positions than those used previously. We also point out that recent computer memory sizes (e.g. 60 GB) make it feasible to use multiple (e.g. eight) seeds for whole mammal genomes. Interestingly, the most sensitive settings achieve diminishing returns for human-dog and melanogaster-pseudoobscura comparisons, but not for human-mouse, which suggests that we still miss many human-mouse alignments. Our optimized heuristics find ∼20,000 new human-mouse alignments that are missing from the standard UCSC alignments. We tabulate seed patterns and parameters that work well so they can be used in future research.
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