ArticleScientific reports2024
Challenges in adjusting scoring matrices when comparing functional motifs with non-standard compositions.
Article in Scientific reports, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 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
2 citing papers in PubMed.
- GBSC: graph-based sequence clustering method for similar short tandem repeats in protein sequences.Bioinformatics (Oxford, England) · 2026Article
- CB-Search: a method for searching for similar protein motifs with biased compositions.BMC bioinformatics · 2026Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
Abstract
Methods for scoring matrix adjustment decrease the significance of biased residues to better detect homology between protein sequences. This is because non-homologous proteins often contain fragments with non-standard compositions that are strikingly similar to each other. However, these fragments are also functionally important in proteins and are receiving an increasing attention from the scientific community. In this study, we described why the gold standard method for scoring matrix adjustment is unable to emphasise frequent amino acids. Further, we used BLAST to align collagen-like domains with and without the scoring matrix adjustment and compared the results. We found that the scoring matrices were adjusted in the opposite direction to the optimal state. Therefore, turning off the adjustment improved alignment quality of collagen-like domains, but scoring matrices still need refinement. This study provides a detailed analysis of why the gold standard method fails, and opens doors for new methods to adjust scoring matrices for functional motifs with non-standard compositions.
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.