LASTZ protocols

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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

 (68)
2018
PMCID: 5850385
PMID: 29438294
DOI: 10.3390/v10020078

[…] 8.0, auckland, new zealand). a multiple alignment analysis of partial genomic regions was performed using the muscle algorithm []. alignments of complete poxvirus genomes were performed using the blastz algorithm []. the alignment file was then used to construct a phylogenetic tree for the tested region, using the mega6 software [], according to the maximum likelihood method., dna […]

2018
PMCID: 5861082
PMID: 29559661
DOI: 10.1038/s41598-018-23196-7

[…] (5′-[a/g]cgtg-3′) were determined using the jaspar core database (http://jaspar.genereg.net/) with a relative score threshold of 0.85. multiz alignment of hre motifs was performed using the ensembl lastz database to analyse species conservation (http://www.ensembl.org/index.html). in addition, we performed bioinformatic analysis of transcription factor binding sites on the 2 kb proximal […]

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

[…] phylofit (siepel et al., ), and the topology was from an angiosperm super-tree (davies et al., ). to generate a pairwise whole-genome alignment against the cucumber genome (huang et al., ), we used lastz (harris, ), 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

[…] (). 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 [], blasr [] and lastz v 1.02.00 [] 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 […]

2018
PMCID: 5870977
PMID: 29584782
DOI: 10.1371/journal.pone.0194253

[…] evident. ()., a pairwise alignment between each pair of genomes was performed to find the overall percent identity. a single, continuous alignment of the entire chromosome could not be achieved with lastz, so a cumulative percent identity was calculated from the multiple segments of alignment and percent coverage of the genome was also calculated in order to clarify what percent of each isolate […]


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LASTZ in publications

 (420)
PMCID: 5943242
PMID: 29743507
DOI: 10.1038/s41598-018-25585-4

[…] v1.2.1. the systematic circular view of the chloroplast genome was created using ogdraw and in-house customized perl script. comparative syntenic maps were generated using circos following the blastz annotation. a chloroplast-based browser was developed for systematic analysis of the chloroplast genomes of the 28 brassica and raphanus genotypes, which can be accessed […]

PMCID: 5923074
PMID: 29491155
DOI: 10.1128/JVI.00135-18

[…] libraries were run according to oxford nanopore protocols v1.3.24 on a singular mk1 (r9.4) flo-min106 flow cell. nanopore reads were mapped to the hhv-6b z29 reference genome (nc_000898) using the lastz and geneious aligners to screen for origin-containing reads (, )., the sequences from this study are available in ncbi genbank (accession numbers mf994813 to mf994829) and associated with ncbi […]

PMCID: 5916904
PMID: 29695739
DOI: 10.1038/s41598-018-24939-2

[…] p. parasitica and p. sojae against the p. cactorum cds library, respectively, in order to find the gene pairs with the best alignments. the resulting orthologous gene pairs were aligned again using lastz with the default parameters as a preparation for kaks_calculator 1.2, which finally yielded a dataset of each gene pair’s ka/ks ratio, and the ka/ks ratio >1 was determined a positively […]

PMCID: 5946948
PMID: 29688346
DOI: 10.1093/gigascience/giy046

[…] relationship among the genomes of medaka, stickleback, and tetraodon to help map the scaffolds on the monopterus chromosomes. the syntenic blocks between monopterus and other fish were aligned by lastz (blastz) [] with parameters of t = 2 and y = 3400. furthermore, we used blat to search for homologous sequences among medaka, sticklebacks, tetraodon, and monopterus in order to fill the gap […]

PMCID: 5924801
PMID: 29740409
DOI: 10.3389/fmicb.2018.00759

[…] (version 34). the repetitive snp was removed by filtration with blast v2.2.2, trf v4.04 and repeatmask v3.2.9 software, and got a reliable snp. the query and reference sequence were compared using lastz v1.01.50 software and results are further optimized with axt_correction, axt_sort and axt_best programs to select the best comparison results. similar to snps, the indel results […]


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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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