Suffix arrays: basic queries
I discuss how to use binary search to query the suffix array. I compare and contrast this with how we queried the suffix tree and compare their time bounds.
These materials are also openly available on figshare. Please cite this work; this ensures that funding agencies see the impact and importance of these open learning materials.
Langmead, Ben (2024). Suffix-based indexing data structures: learning materials. figshare. Collection. https://doi.org/10.6084/m9.figshare.c...
── Course & channel links ──
Course playlist: Suffix Indexing
• Suffix Indexing
Related playlists:
Algorithms for DNA Sequencing: • Algorithms for DNA Sequencing
Burrows-Wheeler Indexing: • Burrows-Wheeler Indexing
── About the author ──
Ben Langmead is a Professor of Computer Science at Johns Hopkins University, where his research spans bioinformatics, computational biology, and data-intensive science. He is the author of Bowtie and Bowtie 2; his group has also developed software like Kraken 2 and resources like recount3 and Index Zone, as well as methods for pangenome indexing and querying, based on e.g. the r-index and move structure. His group's methods have been cited over 130,000 times, and he is the winner of awards including an NSF CAREER award, a Sloan Research Fellowship, the Benjamin Franklin award for contributions to open access, and multiple awards for teaching and mentorship. Ben is the founder and principal of InOrder Labs LLC (https://inorderlabs.com), an expert consulting firm in bioinformatics and computational biology.
Channel: / @benlangmead
Teaching materials: https://langmead-lab.org/teaching.html
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