Searching journal content for articles similar to Joudaki et al..

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  1. Method: Proving sequence aligners can guarantee accuracy in almost O(m log n) time through an average-case analysis of the seed-chain-extend heuristic
    • Jim Shaw and
    • Yun William Yu
    Genome Res. July 2023 33: 1175-1187; Published in Advance March 29, 2023, doi:10.1101/gr.277637.122
    ...-chain-extend with k-mer seeds is a powerful heuristic technique for sequence alignment used by modern sequence aligners. Although effective in practice for both runtime and accuracy, theoretical guarantees on the resulting alignment do not exist for seed-chain-extend. In this work, we give the first rigorous bounds...
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  2. Method: Genomic sketching with multiplicities and locality-sensitive hashing using Dashing 2
    • Daniel N. Baker and
    • Ben Langmead
    Genome Res. July 2023 33: 1218-1227; Published in Advance July 6, 2023, doi:10.1101/gr.277655.123
    ..., which is built by clustering UniRef90 seed sequences from the UniProt Knowledgebase v2021_03 having at least 50% sequence identity to and 80% overlap with the longest sequence in the cluster. The database contains 53,625,855 sequences totaling over 15 billion amino acids. After sketching, the KNN graph...
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  3. Method: Identifying genes within pathways in unannotated genomes with PaGeSearch
    • Sohyoung Won,
    • Jaewoong Yu,
    • and Heebal Kim
    Genome Res. May 2024 34: 784-795; Published in Advance June 10, 2024, doi:10.1101/gr.278566.123
    ...the transcripts in a given list and annotates only relevant sections of the . Also, a recently developed aligner, miniport, that was designed for mapping protein sequences to complete s, integrating modern techniques like k-mer sketch and vectorized dynamic programming, can be used to find particular genes...
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