PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences
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A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
No Canadian affiliation. An affiliation-only frame — the usual design — would never have seen this work. It is one of the works that make the case for inverting the frame.
Machine scores (provisional)
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
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- Teacher spread
- 0.253 · how far apart the two teachers sit on this one work
- Validation status
score_only:v0-immature-baseline· verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it
Abstract
We introduce PASTA, a new multiple sequence alignment algorithm. PASTA uses a new technique to produce an alignment given a guide tree that enables it to be both highly scalable and very accurate. We present a study on biological and simulated data with up to 200,000 sequences, showing that PASTA produces highly accurate alignments, improving on the accuracy and scalability of the leading alignment methods (including SATé). We also show that trees estimated on PASTA alignments are highly accurate--slightly better than SATé trees, but with substantial improvements relative to other methods. Finally, PASTA is faster than SATé, highly parallelizable, and requires relatively little memory.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
The record
- Venue
- Journal of Computational Biology
- Topic
- Genomics and Phylogenetic Studies
- Field
- Biochemistry, Genetics and Molecular Biology
- Canadian institutions
- —
- Funders
- National Institute of General Medical SciencesNational Human Genome Research InstituteHoward Hughes Medical InstituteNational Science FoundationNational Institutes of HealthNational Institute on AgingUniversity of AlbertaPennsylvania Department of Health
- Keywords
- ScalabilityMultiple sequence alignmentParallelizable manifoldComputer scienceSequence (biology)Alignment-free sequence analysisSequence alignmentTree (set theory)AlgorithmComputational biologyData miningBiologyMathematicsPeptide sequenceGenetics
- Has abstract in OpenAlex
- yes