YASS: enhancing the sensitivity of DNA similarity search
By Laurent Noé, Gregory Kucherov. Nucleic Acids Res., 2005
372 citations recorded by the source corpus.
YASS is a DNA local alignment tool based on an efficient and sensitive filtering algorithm. It applies transition-constrained seeds to specify the most probable conserved motifs between homologous sequences, combined with a flexible hit criterion used to identify groups of seeds that are likely to exhibit significant alignments. A web interface () is available to upload input sequences in fasta format, query the program and visualize the results obtained in several forms (dot-plot, tabular output and others). A standalone version is available for download from the web page.
Subfields: Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/4c0c57d9d9b680568cf8d9b1801917a0e4f3094b
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In Molecular Biology
- James D. Lewis
- Jun Chen
- Gary D. Wu
- Frederic D. Bushman
- Andrew Kropinski
- A. Varsani
- Cristina Moraru
- Rob Knight
In Plant Science
Citations in the corpus
- VIRIDIC—A Novel Tool to Calculate the Intergenomic Similarities of Prokaryote-Infecting Viruses (2020, methodology): “…et al. 2016), KI-S tool (https://f1000research.com/posters/7-147), PAirwise Sequence Comparison (PASC; (Bao et al. 2012; Bao et al. 2014), Sequence Demarcation Tool (SDT; (Muhire et al. 2014), Simka (https://arxiv.org/abs/1604.02412), Yet Another Similarity Searcher (YASS; (Noé and Kucherov 2005).”
- The human gut virome: inter-individual variation and dynamic response to diet. (2011, methodology): “Similarity between VLP contigs was assessed using YASS (Noe and Kucherov 2005), a DNA local alignment tool.”