ArticleProceedings of the National Academy of Sciences of the United States of America2004
Comparative homology agreement search: an effective combination of homology-search methods.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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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.
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Who cites it
7 citing papers in PubMed.
- Article
- Improved performance of sequence search approaches in remote homology detection.F1000Research · 2013Article
- Biodefense Oriented Genomic-Based Pathogen Classification Systems: Challenges and Opportunities.Journal of bioterrorism & biodefense · 2012Article
- Learning biomarkers of pluripotent stem cells in mouse.DNA research : an international journal for rapid publication of reports on genes and genomes · 2011Article
- TransportTP: a two-phase classification approach for membrane transporter prediction and characterization.BMC bioinformatics · 2009Article
- Homology and phylogeny and their automated inference.Die Naturwissenschaften · 2008Review
- Comparative genome analysis across a kingdom of eukaryotic organisms: specialization and diversification in the fungi.Genome research · 2007Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many methods have been developed to search for homologous members of a protein family in databases, and the reliability of results and conclusions may be compromised if only one method is used, neglecting the others. Here we introduce a general scheme for combining such methods. Based on this scheme, we implemented a tool called comparative homology agreement search (chase) that integrates different search strategies to obtain a combined "E value." Our results show that a consensus method integrating distinct strategies easily outperforms any of its component algorithms. More specifically, an evaluation based on the Structural Classification of Proteins database reveals that, on average, a coverage of 47% can be obtained in searches for distantly related homologues (i.e., members of the same superfamily but not the same family, which is a very difficult task), accepting only 10 false positives, whereas the individual methods obtain a coverage of 28-38%.
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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.