Suffix trees: basic queries

Here I discuss basic algorithms for querying the suffix tree along with their time complexities. These include queries that check for presence or absence of substrings, queries the count the number of times a substring occurs, and queries that report all offsets where a substring occurs.

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Langmead, Ben (2024). Suffix-based indexing data structures: learning materials. figshare. Collection. https://doi.org/10.6084/m9.figshare.c...

Channel: ‪@BenLangmead‬
Playlist:    • Suffix Indexing  
Related playlist with videos on pattern matching and substring indexes:    • Algorithms for DNA Sequencing  
Related playlist with videos on Burrows-Wheeler indexing approaches:    • Burrows-Wheeler Indexing  
More materials: http://www.langmead-lab.org/teaching-...