ArticleBioinformatics (Oxford, England)2015
Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed.
- NNKcat: deep neural network to predict catalytic constants (Kcat) by integrating protein sequence and substrate structure with enhanced data imbalance handling.Briefings in bioinformatics · 2025Article
- Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives.Briefings in bioinformatics · 2025Review
- HFTC: a hierarchical fungal taxonomic classification model for ITS sequences using low-dimensional embedding features.Frontiers in genetics · 2025Article
- REDalign: accurate RNA structural alignment using residual encoder-decoder network.BMC bioinformatics · 2024Article
- VirusPredictor: XGBoost-based software to predict virus-related sequences in human data.Bioinformatics (Oxford, England) · 2024Article
- BiComp-DTA: Drug-target binding affinity prediction through complementary biological-related and compression-based featurization approach.PLoS computational biology · 2023Article
- A toolbox of machine learning software to support microbiome analysis.Frontiers in microbiology · 2023Review
- G-SAIP: Graphical Sequence Alignment Through Parallel Programming in the Post-Genomic Era.Evolutionary bioinformatics online · 2023Article
- Emerging Computational Approaches for Antimicrobial Peptide Discovery.Antibiotics (Basel, Switzerland) · 2022Review
- Determination of k-mer density in a DNA sequence and subsequent cluster formation algorithm based on the application of electronic filter.Scientific reports · 2021Article
- A case study of salivary microbiome in smokers and non-smokers in Hungary: analysis by shotgun metagenome sequencing.Journal of oral microbiology · 2020Article
- An Introduction to Machine Learning.Clinical pharmacology and therapeutics · 2020Review
- Specificity Analysis of Genome Based on Statistically Identical K-Words With Same Base Combination.IEEE open journal of engineering in medicine and biology · 2020Article
- Graph Theory-Based Sequence Descriptors as Remote Homology Predictors.Biomolecules · 2019Article
- A survey and evaluations of histogram-based statistics in alignment-free sequence comparison.Briefings in bioinformatics · 2019Article
- DisCVR: Rapid viral diagnosis from high-throughput sequencing data.Virus evolution · 2019Article
- Insights of Window-Based Mechanism Approach to Visualize Composite BioData Point in Feature Spaces.Genomics & informatics · 2019Article
- Surveying alignment-free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers.BMC bioinformatics · 2018Article
- Protein Sequence Comparison Based on Physicochemical Properties and the Position-Feature Energy Matrix.Scientific reports · 2017Article
- CSSSCL: a python package that uses combined sequence similarity scores for accurate taxonomic classification of long and short sequence reads.Bioinformatics (Oxford, England) · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationAlignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized.
resultsOur model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences. AVAILABILITY AND IMPLEMENTATION: All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html. CONTACT: ivan.borozan@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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.