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