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Protocols

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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Versioning


No version available

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 citations

 (521)
library_books

Re exploration of U’s Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences

2018
Sci Rep
PMCID: 5943242
PMID: 29743507
DOI: 10.1038/s41598-018-25585-4

[…] can-SE 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 at www.phyzen.co.kr/cpb […]

library_books

Copy Number Heterogeneity, Large Origin Tandem Repeats, and Interspecies Recombination in Human Herpesvirus 6A (HHV 6A) and HHV 6B Reference Strains

2018
J Virol
PMCID: 5923074
PMID: 29491155
DOI: 10.1128/JVI.00135-18

[…] ed 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 (, ). […]

library_books

The Phytophthora cactorum genome provides insights into the adaptation to host defense compounds and fungicides

2018
Sci Rep
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 selected […]

library_books

Chromosome scale assembly of the Monopterus genome

2018
GigaScience
PMCID: 5946948
PMID: 29688346
DOI: 10.1093/gigascience/giy046

[…] nic 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 seq […]

call_split

Enhanced Fluorescent Siderophore Biosynthesis and Loss of Phenazine 1 Carboxamide in Phenotypic Variant of Pseudomonas chlororaphis HT66

2018
Front Microbiol
PMCID: 5924801
PMID: 29740409
DOI: 10.3389/fmicb.2018.00759
call_split See protocol

[…] ST (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 were further ver […]

library_books

Inter genome comparison of the Quorn fungus Fusarium venenatum and the closely related plant infecting pathogen Fusarium graminearum

2018
BMC Genomics
PMCID: 5907747
PMID: 29673315
DOI: 10.1186/s12864-018-4612-2

[…] ly, the software SOAPdenovo2 (version 2.0.4) was used with different k-mer values: 61–91. Reference sequence statistics were extracted from Tablet and Geneious [] (version 9.1 created by Biomatters). Lastz (version 1.02.00) and Mauve (version 2.3.1) was used from within Geneious to align genomic sequences to F. graminearum (ENA study accession: PRJEB5475). […]

Citations

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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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