ArticleEvolutionary bioinformatics online2013
SARP: A Novel Algorithm to Assess Compositional Biases in Protein Sequences.
Article in Evolutionary bioinformatics online, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
9 citing papers in PubMed.
- C-Terminal Regions of Insecticidal Cry Toxins Form Amyloid Fibrils Affecting Metabolism of Insect Cells.International journal of molecular sciences · 2026Article
- Optimizing strategy for the discovery of compositionally-biased or low-complexity regions in proteins.Scientific reports · 2024Article
- Application of yeast to studying amyloid and prion diseases.Advances in genetics · 2020Review
- Biomolecular Assemblies: Moving from Observation to Predictive Design.Chemical reviews · 2018Review
- Exploring Proteins Containing Amyloidogenic Regions in the Proteomes of Bacteria of the OrderEvolutionary bioinformatics online · 2018Article
- M60-like metalloprotease domain of the Escherichia coli YghJ protein forms amyloid fibrils.PloS one · 2018Article
- Predicting Amyloidogenic Proteins in the Proteomes of Plants.International journal of molecular sciences · 2017Article
- Review
- Prions, amyloids, and RNA: Pieces of a puzzle.Prion · 2016Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The composition of a defined set of subunits (nucleotides, amino acids) is one of the key features of biological sequences. Compositional biases are local shifts in amino acid or nucleotide frequencies that can occur as an adaptation of an organism to an extreme ecological niche, or as the signature of a specific function or localization of the corresponding protein. The calculation of probability is a method for annotating compositional bias and providing accurate detection of biased subsequences. Here, we present a Sequence Analysis based on the Ranking of Probabilities (SARP), a novel algorithm for the annotation of compositional biases based on ranking subsequences by their probabilities. SARP provides the same accuracy as the previously published Lower Probability Subsequences (LPS) algorithm but performs at an approximately 230-fold faster rate. It can be recommended for use when working with large datasets to reduce the time and resources required.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.