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GLAM2Scan specifications

Information


Unique identifier OMICS_08379
Name GLAM2Scan
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data GLAM2 motifs, DNA/Protein sequences
Operating system Unix/Linux
Computer skills Advanced
Version 4.10.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline FIMO Team

Information


Unique identifier OMICS_08379
Name GLAM2Scan
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data GLAM2 motifs, DNA/Protein sequences
Computer skills Basic
Version 4.10.1
Stability Stable
Maintained Yes

Maintainer


  • person_outline FIMO Team

Publication for GLAM2Scan

GLAM2Scan citations

 (14)
library_books

In silico analyses of conservational, functional and phylogenetic distribution of the LuxI and LuxR homologs in Gram positive bacteria

2017
Sci Rep
PMCID: 5539150
PMID: 28765541
DOI: 10.1038/s41598-017-07241-5

[…] of Motifs) software in putative LuxI/LuxR proteins of Gram-positive bacteria. Furthermore, the scanning of extracted motif in a sequence database (LuxI/LuxR of Gram-negative bacteria) was done using GLAM2SCAN v1056 software. The high intensity of the GLAM2 score for particular motif indicates its strength. […]

library_books

The Global Redox Responding RegB/RegA Signal Transduction System Regulates the Genes Involved in Ferrous Iron and Inorganic Sulfur Compound Oxidation of the Acidophilic Acidithiobacillus ferrooxidans

2017
Front Microbiol
PMCID: 5506826
PMID: 28747899
DOI: 10.3389/fmicb.2017.01277

[…] MEME suite (Bailey et al., ). The obtained motifs were then compared to known motifs of prokaryotic transcription factors (Gupta et al., ), and finally searched within the ATCC 23270T genome with the GLAM2SCAN tool [(Frith et al., ); MEME suite (Bailey et al., )]. […]

library_books

Antibiotic Capture by Bacterial Lipocalins Uncovers an Extracellular Mechanism of Intrinsic Antibiotic Resistance

2017
MBio
PMCID: 5350466
PMID: 28292982
DOI: 10.1128/mBio.00225-17

[…] Motifs GLAM2 tool (). This motif was verified by analyzing an alignment of 1,995 BCN homologues with CLUSTAL-omega and visualized with JalView. In addition, upon submitting the predicted motif to the GLAM2Scan database () against B. cenocepacia, P. aeruginosa PAO1, M. tuberculosis H37Rv, and S. aureus USA300, the correct homologues only were detected as BCNs for each of the organisms. […]

library_books

Crystal structure and DNA binding activity of a PadR family transcription regulator from hypervirulent Clostridium difficile R20291

2016
BMC Microbiol
PMCID: 5050560
PMID: 27716049
DOI: 10.1186/s12866-016-0850-0

[…] iction since spacing between the inverted repeats was not critical for binding. The best motif was 21 bp in length with the sequence GTACTAT(N2)ATTATA(N)AGTA and was designated cdPadR1 motif (Fig. ). GLAM2Scan results indicated the presence of 200 potential motif matches in the C. difficile strain R20291 genome with scores ranging from 13.6–18.7, not including the PcdpadR1 sequences used for analy […]

library_books

Systematic protein interactome analysis of glycosaminoglycans revealed YcbS as a novel bacterial virulence factor

2016
Sci Rep
PMCID: 4914927
PMID: 27323865
DOI: 10.1038/srep28425

[…] the FASTA format and analysed using GLAM2 to survey consensus motifs. The GLAM2 parameters were set as the default, and the resulting motifs were searched through the entire E. coli proteome by using GLAM2SCAN. […]

library_books

'PP2C7s', Genes Most Highly Elaborated in Photosynthetic Organisms, Reveal the Bacterial Origin and Stepwise Evolution of PPM/PP2C Protein Phosphatases

2015
PLoS One
PMCID: 4524716
PMID: 26241330
DOI: 10.1371/journal.pone.0132863

[…] utput and displayed in GeneDoc). Inferred GLAM2 motifs were used to search the NCBI non-redundant protein database using GLAM2SCAN (Scanning with Gapped Motifs) ([]; http://meme.nbcr.net/meme/cgi-bin/glam2scan.cgi). […]

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GLAM2Scan institution(s)
Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan

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