LASTZ pipeline

LASTZ specifications

Information


Unique identifier OMICS_19095
Name LASTZ
Alternative name BLASTZ
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C
License MIT License
Computer skills Advanced
Version 1.04.00
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Webb Miller <>

Additional information


http://www.bx.psu.edu/~rsharris/lastz/README.lastz-1.04.00.html

Publication for LASTZ

LASTZ IN pipelines

 (38)
2018
PMCID: 5821093
PMID: 29440577
DOI: 10.1128/mBio.02381-17

[…] new zealand). sequence features were annotated using the geneious 8 annotation transfer tool, and sequences were aligned using a combination of blast (29), muscle (30), progressive mauve (31), and lastz alignment tools. average nucleotide identity data were calculated using blast (anib) and jspecies (32), core genome alignments were performed using panseq (33), and phylogenetic trees […]

2018
PMCID: 5863696
PMID: 29599790
DOI: 10.3389/fpls.2018.00325

[…] et al., 2005), and the topology was from an angiosperm super-tree (davies et al., 2004). to generate a pairwise whole-genome alignment against the cucumber genome (huang et al., 2009), we used lastz (harris, 2007), a local alignment algorithm optimized for whole-genome alignments, to locally compare the cucumber reference genome with all of the sequences of each query genome. then, […]

2018
PMCID: 5864009
PMID: 29566006
DOI: 10.1371/journal.pone.0194366

[…] 2). in both experiments, reads had a length spanning from 226 bp to 20,498 bp with a mean of ~5,600 kb that includes sequences of hbv and vector. available aligners last v475 [15], blasr [19] and lastz v 1.02.00 [20] were tested to align nanopore reads to their respective sanger sequence references including hbv and vector sequences. last was the read aligner generating the largest number […]

2017
PMCID: 5737078
PMID: 28645144
DOI: 10.1093/nar/gkx554

[…] genome. all intact exons of a gene were grouped into a gene model., to investigate the effect of alignment parameter sensitivity on detecting alignments between exons of orthologous genes, we used lastz (20) and evaluated three different alignment parameter sets (table 1) that differ in the score threshold of ungapped high-scoring segment pairs (parameter k) and the score threshold […]

2017
PMCID: 5751788
PMID: 29297287
DOI: 10.1186/s12859-017-1902-7

[…] of the most widely used bioinformatics applications is basic local alignment search tool (blast) from the national institute of health [1]. blast [2] and its many variants (blastn, blastp, blastx, blastz, etc.) are used by more scientists than any other bioinformatics application [3]. the blast family of programs is used to address a fundamental problem in bioinformatics research: sequence […]

LASTZ institution(s)
Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA, USA; Institute for Systems Biology, Seattle, WA, USA; Paracel Inc., Pasadena, CA, USA; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, CA, USA
LASTZ funding source(s)
Supported by grant HG-02238 from the National Human Genome Research Institute, with additional support from NIH grant RO1 DK27635; NHGRI Grant 1P41HG02371.

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