ArticleBioinformatics (Oxford, England)2014
Frameshift alignment: statistics and post-genomic applications.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- DANTE and DANTE_LTR: lineage-centric annotation pipelines for long terminal repeat retrotransposons in plant genomes.NAR genomics and bioinformatics · 2024Article
- Sensitive and error-tolerant annotation of protein-coding DNA with BATH.bioRxiv : the preprint server for biology · 2024Article
- Sensitive and error-tolerant annotation of protein-coding DNA with BATH.Bioinformatics advances · 2024Article
- MAIRA: Protein-based Analysis of MinION Reads on a Laptop.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Article
- Paleozoic Protein Fossils Illuminate the Evolution of Vertebrate Genomes and Transposable Elements.Molecular biology and evolution · 2022Article
- Assembly-free rapid differential gene expression analysis in non-model organisms using DNA-protein alignment.BMC genomics · 2022Article
- Improved Large-Scale Homology Search by Two-Step Seed Search Using Multiple Reduced Amino Acid Alphabets.Genes · 2021Article
- Application of computational approaches to analyze metagenomic data.Journal of microbiology (Seoul, Korea) · 2021Review
- Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples.NPJ science of food · 2021Article
- MAIRA- real-time taxonomic and functional analysis of long reads on a laptop.BMC bioinformatics · 2020Article
- Expanded genome-wide comparisons give novel insights into population structure and genetic heterogeneity of Leishmania tropica complex.PLoS neglected tropical diseases · 2020Article
- PHANOTATE: a novel approach to gene identification in phage genomes.Bioinformatics (Oxford, England) · 2019Article
- Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps.Nature communications · 2019Article
- Search for potential reading frameshifts in cds from Arabidopsis thaliana and other genomes.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- RIFRAF: a frame-resolving consensus algorithm.Bioinformatics (Oxford, England) · 2018Article
- Parallels between experimental and natural evolution of legume symbionts.Nature communications · 2018Article
- MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs.Biology direct · 2018Article
- Companion: a web server for annotation and analysis of parasite genomes.Nucleic acids research · 2016Article
- ALP & FALP: C++ libraries for pairwise local alignment E-values.Bioinformatics (Oxford, England) · 2016Article
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4 authors.
Funding
Abstract
motivationThe alignment of DNA sequences to proteins, allowing for frameshifts, is a classic method in sequence analysis. It can help identify pseudogenes (which accumulate mutations), analyze raw DNA and RNA sequence data (which may have frameshift sequencing errors), investigate ribosomal frameshifts, etc. Often, however, only ad hoc approximations or simulations are available to provide the statistical significance of a frameshift alignment score.
resultsWe describe a method to estimate statistical significance of frameshift alignments, similar to classic BLAST statistics. (BLAST presently does not permit its alignments to include frameshifts.) We also illustrate the continuing usefulness of frameshift alignment with two 'post-genomic' applications: (i) when finding pseudogenes within the human genome, frameshift alignments show that most anciently conserved non-coding human elements are recent pseudogenes with conserved ancestral genes; and (ii) when analyzing metagenomic DNA reads from polluted soil, frameshift alignments show that most alignable metagenomic reads contain frameshifts, suggesting that metagenomic analysis needs to use frameshift alignment to derive accurate results.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.