Improved pairwise alignment of genomic dna

By Robert S. Harris. 2007

1,227 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/8392ce0242d4a969525e668b3747470e64b350d8

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Citations in the corpus

Identifying conserved genomic elements and designing universal bait sets to enrich them (2017, methodology): “set to each genome using a wrapper (phyluce_probe_run_multiple_lastzs_sqlite) around lastz (Harris 2007) with liberal alignment parameters (≥50% sequence identity required tomap).”
Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020, unknown): “The subproblem procedure begins with a set of pairwise local alignments generated via the sensitive pairwise local-alignment program LASTZ [24].”
The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000 (2018, methodology): “2) and the common wombat (vu-1k) and Virginia opossum (dv-1k) de novo assemblies were aligned using the LastZ alignment algorithm (Robert S. Harris 2007) using “--notransition --step=20 –nogapped” command options; the gray-tailed opossum genome assembly was used as a target.”
Ensembl comparative genomics resources (2016, methodology): “LASTZ-net alignments are sorted on a reference genome (grey).”
Enriching the ant tree of life: enhanced UCE bait set for genome‐scale phylogenetics of ants and other Hymenoptera (2017, methodology): “rosae using a wrapper (phyluce_probe_run_multiple_lastzs_sqlite) around LASTZ (Harris 2007) with liberal alignment parameters (≥50% sequence identity required tomap).”
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species (2013, methodology): “Alignment lengths are derived from Lastz alignments of scaffold sequences from each assembly to the bird Fosmid sequences.”
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences (2015, methodology): “It is adapted from Kahn’s topological sorting algorithm (Kahn, 1962). It starts from the potential source and visits a vertex when all its incoming edges are visited before. Algorithm 6 only detects bubbles. We can keep track of the optimal parent vertex at line 1 and then backtrack to collapse bubb”
Ensembl Genomes 2016: more genomes, more complexity (2015, methodology): “Closely related eukaryotic species are identified as suitable subjects for pairwise whole genome alignment, normally carried out using the lastZ (22) alignment tool followed by chaining and netting (23).”