X-Mapper: fast and accurate sequence alignment via gapped x-mers
Sequence alignment is foundational to many bioinformatic analyses. Many aligners start by splitting sequences into contiguous, fixed-length seeds, called k-mers. Alignment is faster with longer, unique seeds, but more accurate with shorter seeds avoiding mutations. Here, we introduce X-Mapper, aimin...
| Main Authors: | , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
BioMed Central
2025
|
| Online Access: | https://hdl.handle.net/1721.1/158285 |
| _version_ | 1826214970760626176 |
|---|---|
| author | Gaston, Jeffry M. Alm, Eric J. Zhang, An-Ni |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Gaston, Jeffry M. Alm, Eric J. Zhang, An-Ni |
| author_sort | Gaston, Jeffry M. |
| collection | MIT |
| description | Sequence alignment is foundational to many bioinformatic analyses. Many aligners start by splitting sequences into contiguous, fixed-length seeds, called k-mers. Alignment is faster with longer, unique seeds, but more accurate with shorter seeds avoiding mutations. Here, we introduce X-Mapper, aiming to offer high speed and accuracy via dynamic-length seeds containing gaps, called gapped x-mers. We observe 11–24-fold fewer suboptimal alignments analyzing a human reference and 3–579-fold lower inconsistency across bacterial references than other aligners, improving on 53% and 30% of reads aligned to non-target strains and species, respectively. Other seed-based analysis algorithms might benefit from gapped x-mers too. |
| first_indexed | 2025-03-10T13:45:13Z |
| format | Article |
| id | mit-1721.1/158285 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2025-03-10T13:45:13Z |
| publishDate | 2025 |
| publisher | BioMed Central |
| record_format | dspace |
| spelling | mit-1721.1/1582852025-03-03T17:44:16Z X-Mapper: fast and accurate sequence alignment via gapped x-mers Gaston, Jeffry M. Alm, Eric J. Zhang, An-Ni Massachusetts Institute of Technology. Department of Biological Engineering Sequence alignment is foundational to many bioinformatic analyses. Many aligners start by splitting sequences into contiguous, fixed-length seeds, called k-mers. Alignment is faster with longer, unique seeds, but more accurate with shorter seeds avoiding mutations. Here, we introduce X-Mapper, aiming to offer high speed and accuracy via dynamic-length seeds containing gaps, called gapped x-mers. We observe 11–24-fold fewer suboptimal alignments analyzing a human reference and 3–579-fold lower inconsistency across bacterial references than other aligners, improving on 53% and 30% of reads aligned to non-target strains and species, respectively. Other seed-based analysis algorithms might benefit from gapped x-mers too. 2025-03-03T17:39:10Z 2025-03-03T17:39:10Z 2025-01-22 2025-02-13T10:17:37Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/158285 Gaston, J.M., Alm, E.J. & Zhang, AN. X-Mapper: fast and accurate sequence alignment via gapped x-mers. Genome Biol 26, 15 (2025). PUBLISHER_CC en https://doi.org/10.1186/s13059-024-03473-7 Genome Biology Creative Commons Attribution https://creativecommons.org/licenses/by/4.0/ The Author(s) application/pdf application/pdf BioMed Central BioMed Central |
| spellingShingle | Gaston, Jeffry M. Alm, Eric J. Zhang, An-Ni X-Mapper: fast and accurate sequence alignment via gapped x-mers |
| title | X-Mapper: fast and accurate sequence alignment via gapped x-mers |
| title_full | X-Mapper: fast and accurate sequence alignment via gapped x-mers |
| title_fullStr | X-Mapper: fast and accurate sequence alignment via gapped x-mers |
| title_full_unstemmed | X-Mapper: fast and accurate sequence alignment via gapped x-mers |
| title_short | X-Mapper: fast and accurate sequence alignment via gapped x-mers |
| title_sort | x mapper fast and accurate sequence alignment via gapped x mers |
| url | https://hdl.handle.net/1721.1/158285 |
| work_keys_str_mv | AT gastonjeffrym xmapperfastandaccuratesequencealignmentviagappedxmers AT almericj xmapperfastandaccuratesequencealignmentviagappedxmers AT zhanganni xmapperfastandaccuratesequencealignmentviagappedxmers |