Lasergene Genomics Suite protocols

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Lasergene Genomics Suite specifications

Information


Unique identifier OMICS_01125
Name Lasergene Genomics Suite
Alternative names Lasergene’s DNA SeqMan software, Lasergene
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
High performance computing Yes
Free trial Yes
Maintained Yes

Subtools


  • ArrayStar
  • GenVision Pro
  • Molecular Biology Suite
  • SeqMan NGen

Versioning


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Documentation


Additional information


A basic version, Lasergene Genomics Essentials Software, is also available at http://www.dnastar.com/t-products-lasergene-genomics-essentials.aspx Tutorials http://www.dnastar.com/t-support-tutorials.aspx

Lasergene Genomics Suite in pipelines

 (42)
2018
PMCID: 5814480
PMID: 29449399
DOI: 10.1128/genomeA.01461-17

[…] blood and tissue kit (catalog no. 69506). sequence data were generated from a 100-bp paired-end library on the illumina hiseq 2000 platform. the sequence reads were assembled de novo using dnastar seqman ngen version 12 software into an average of 63.8 contigs (range, 35 to 113). the mauve aligner was used to reorder the contigs (). the assembled draft genomes contained an average g+c content […]

2018
PMCID: 5875261
PMID: 29400646
DOI: 10.3201/eid2404.171919

[…] and sequenced them on the ion torrent personal genomics machine instrument using the ion pgm hi-q sequencing kit (life technologies). we generated full genome sequences using a templated assembly in seqman ngen (dnastar, madison, wi, usa) and using zika virus strain prvabc-59 (genbank accession no. kx377337) as a reference. we subjected consensus genomes generated by templated assemblies […]

2018
PMCID: 5932376
PMID: 29720527
DOI: 10.1128/mSphere.00464-17

[…] and analyze in silico amplicons. for 10 isolates for which conventional typing and wgs typing results were discordant, raw read data were aligned to sequences of several sccmec cassette types using seqman ngen v.12.1.0 (dnastar, madison, wi). types were confirmed by read coverage breadth and depth against the reference sccmec type sequences., snps that differentiate specific clades of s. aureus […]

2017
PMCID: 5261728
PMID: 28118395
DOI: 10.1371/journal.pone.0170734

[…] phages was sequenced using ion torrent™ next-gen sequencing technology (life technologies, carlsbad, usa) at seqomics biotechnology ltd (mórahalom, hungary). all genomes were assembled de novo using seqman ngen software from a lasergene v.10 genomics package (dnastar, madison, usa). genomes were annotated using rast (rapid annotation using subsystem technology), a fully-automatic annotation […]

2017
PMCID: 5328969
PMID: 28293249
DOI: 10.3389/fpls.2017.00271

[…] using cd-hit-est () using 90% similarity and a word size of 8. transdecoder () and blast2go () were used to predict protein-coding sequences., the single-end sequenced library were mapped using the arraystar application and qseq module of the dnastar lasergene genomics suite (version 11; dnastar, inc., madison, wi, usa) with all parameters set to defaults. qseq parameters were set to default, […]


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Lasergene Genomics Suite in publications

 (684)
PMCID: 5930841
PMID: 29743953
DOI: 10.1186/s13068-018-1116-x

[…] nextclip processed mate-pair reads. assembly statistics were collected using assemblathon_stats.pl []. gaps in the scaffolds were then filled in by mapping the reads to the allpaths-lg scaffolds and seqman ngen software (dnastar inc., madison, wisconsin, usa)., alternatively, at nrel and hubei university, the quality of fastq genome resequencing data was checked using fastqc program, data […]

PMCID: 5932376
PMID: 29720527
DOI: 10.1128/mSphere.00464-17

[…] and analyze in silico amplicons. for 10 isolates for which conventional typing and wgs typing results were discordant, raw read data were aligned to sequences of several sccmec cassette types using seqman ngen v.12.1.0 (dnastar, madison, wi). types were confirmed by read coverage breadth and depth against the reference sccmec type sequences., snps that differentiate specific clades of s. aureus […]

PMCID: 5930724
PMID: 29720189
DOI: 10.1186/s12943-018-0829-6

[…] subjects have written informed consent and this study was approved by the institutional review boards of nanjing medical university., the lncrna expression characteristics of gc were investigated by arraystar human lncrna microarray v2.0, which contains 30,215 coding genes and 33,045 lncrnas collected from several databases such as ucsc, ensembl, refseq and the lncrnas reported from literatures […]

PMCID: 5930968
PMID: 29716593
DOI: 10.1186/s12943-018-0833-x

[…] through mirna sequestration [], putative circrna/mirna interactions for the 12 differential circrnas identified from the microarray and qrt-pcr validation experiments were predicted using the arraystar mirna target prediction software (arraystar), based on targetscan and miranda algorithms []. the arraystar software was then used to search for mres on the 12 differential circrnas […]

PMCID: 5928226
PMID: 29712904
DOI: 10.1038/s41467-018-04010-4

[…] dnase treatment using the rnase-free dnase set. rna quantity and quality were assessed by a nanodrop nd-1000, with rna integrity determined by standard denaturing agarose gel electrophoresis. arraystar human lncrna microarray v3.0 designed for global profiling of human lncrnas (32,586) and protein-coding transcripts (26,109) covering all entries of refseq, ucsc known genes and gencode […]


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