LAGAN protocols

LAGAN specifications

Information


Unique identifier OMICS_08469
Name LAGAN
Alternative names M-LAGAN, Shuffle-LAGAN, Multi-LAGAN, SLAGAN
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Serafim Batzoglou <>

Information


Unique identifier OMICS_08469
Name LAGAN
Alternative names M-LAGAN, Shuffle-LAGAN, Multi-LAGAN, SLAGAN
Software type Application/Script, Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.0
Stability Stable
Source code URL http://lagan.stanford.edu/lagan_web/lagan20.tar.gz
Maintained Yes

Versioning


Add your version

Maintainer


  • person_outline Serafim Batzoglou <>

Publications for LAGAN

LAGAN IN pipelines

 (12)
2018
PMCID: 5920332
PMID: 29514290
DOI: 10.1093/jxb/ery083

[…] 1 kb region upstream of the translational start site using phytozome genomic data and alignments were performed by using blastn, with the recommended parameters described by kaplinsky et al. (2002), lagan (brudno et al., 2003), and mulan (ovcharenko et al., 2005) algorithms. conserved promoter elements present in at least three different species, including sugarcane, were considered […]

2015
PMCID: 4551851
PMID: 26313368
DOI: 10.1371/journal.pone.0136666

[…] assembly, nov 2009), coelacanth (latcha1, insdc assembly, sep 2011), medaka (hdrr, oct 2005) and spotted gar (lepocu1, insdc assembly, dec 2011). global pairwise alignment was carried out using shuffle-lagan [32], and the results were visualized using the vista browser [33]. conserved transcription factor binding consensus sequences were identified using rvista [34] and visual inspection […]

2015
PMCID: 4551851
PMID: 26313368
DOI: 10.1371/journal.pone.0136666

[…] nov 2009), coelacanth (latcha1, insdc assembly, sep 2011), medaka (hdrr, oct 2005) and spotted gar (lepocu1, insdc assembly, dec 2011). global pairwise alignment was carried out using shuffle-lagan [32], and the results were visualized using the vista browser [33]. conserved transcription factor binding consensus sequences were identified using rvista [34] and visual inspection […]

2012
PMCID: 3264657
PMID: 22292071
DOI: 10.1371/journal.pone.0030895

[…] respectively [61]. tarsier (tarsius syrichta) sequences were identified from the whole-genome shotgun sequence database in ncbi using blastn [62]. sequence alignment was performed using multi-lagan [63] and visualized in bioedit [64]. p-match [65] was used for identification and scoring of yy1 dna response elements. matching was performed to predefined vertebrate matrices in a liver […]

2012
PMCID: 3264657
PMID: 22292071
DOI: 10.1371/journal.pone.0030895

[…] respectively [61]. tarsier (tarsius syrichta) sequences were identified from the whole-genome shotgun sequence database in ncbi using blastn [62]. sequence alignment was performed using multi-lagan [63] and visualized in bioedit [64]. p-match [65] was used for identification and scoring of yy1 dna response elements. matching was performed to predefined vertebrate matrices in a liver […]

LAGAN institution(s)
Department of Computer Science, Stanford University, Stanford, CA, USA; Department of Pathology and Department of Genetics, Stanford University, Stanford, CA, USA; Genome Technology Branch and NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
LAGAN funding source(s)
Supported by an NSF Graduate Fellowship; a Howard Hughes Medical Institute predoctoral fellowship; and funds from the National Human Genome Research Institute.

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