{"paper":{"title":"Succincter Text Indexing with Wildcards","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["q-bio.QM"],"primary_cat":"cs.DS","authors_text":"Chris Thachuk","submitted_at":"2011-01-27T20:09:34Z","abstract_excerpt":"We study the problem of indexing text with wildcard positions, motivated by the challenge of aligning sequencing data to large genomes that contain millions of single nucleotide polymorphisms (SNPs)---positions known to differ between individuals. SNPs modeled as wildcards can lead to more informed and biologically relevant alignments. We improve the space complexity of previous approaches by giving a succinct index requiring $(2 + o(1))n \\log \\sigma + O(n) + O(d \\log n) + O(k \\log k)$ bits for a text of length $n$ over an alphabet of size $\\sigma$ containing $d$ groups of $k$ wildcards. A key"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1101.5376","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}