ArticleNucleic acids research2008
The whole alignment and nothing but the alignment: the problem of spurious alignment flanks.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- 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
- Paleozoic Protein Fossils Illuminate the Evolution of Vertebrate Genomes and Transposable Elements.Molecular biology and evolution · 2022Article
- TMRS: an algorithm for computing the time to the most recent substitution event from a multiple alignment column.Algorithms for molecular biology : AMB · 2019Article
- HFSP: high speed homology-driven function annotation of proteins.Bioinformatics (Oxford, England) · 2018Article
- MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets.Nature biotechnology · 2017Article
- Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix.Journal of structural and functional genomics · 2016Article
- The Dfam database of repetitive DNA families.Nucleic acids research · 2016Article
- Split-alignment of genomes finds orthologies more accurately.Genome biology · 2015Article
- A call for benchmarking transposable element annotation methods.Mobile DNA · 2015Article
- Mammalian NUMT insertion is non-random.Nucleic acids research · 2012Article
- Article
- Genome-wide synteny through highly sensitive sequence alignment: Satsuma.Bioinformatics (Oxford, England) · 2010Article
- Cgaln: fast and space-efficient whole-genome alignment.BMC bioinformatics · 2010Article
- Parameters for accurate genome alignment.BMC bioinformatics · 2010Article
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Authors and funding
4 authors.
Funding
Abstract
Pairwise sequence alignment is a ubiquitous tool for inferring the evolution and function of DNA, RNA and protein sequences. It is therefore essential to identify alignments arising by chance alone, i.e. spurious alignments. On one hand, if an entire alignment is spurious, statistical techniques for identifying and eliminating it are well known. On the other hand, if only a part of the alignment is spurious, elimination is much more problematic. In practice, even the sizes and frequencies of spurious subalignments remain unknown. This article shows that some common scoring schemes tend to overextend alignments and generate spurious alignment flanks up to hundreds of base pairs/amino acids in length. In the UCSC genome database, e.g. spurious flanks probably comprise >18% of the human-fugu genome alignment. To evaluate the possibility that chance alone generated a particular flank on a particular pairwise alignment, we provide a simple 'overalignment' P-value. The overalignment P-value can identify spurious alignment flanks, thereby eliminating potentially misleading inferences about evolution and function. Moreover, by explicitly demonstrating the tradeoff between over- and under-alignment, our methods guide the rational choice of scoring schemes for various alignment tasks.
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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.