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Protocols

MetaLocGramN specifications

Information


Unique identifier OMICS_01626
Name MetaLocGramN
Interface Web user interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Magnus Marcin

Publication for MetaLocGramN

MetaLocGramN citations

 (7)
library_books

Pangenome and immuno proteomics analysis of Acinetobacter baumannii strains revealed the core peptide vaccine targets

2016
BMC Genomics
PMCID: 5025611
PMID: 27634541
DOI: 10.1186/s12864-016-2951-4

[…] a limitation of the tool itself, not with the overall pipeline; therefore it is suggested that the researcher should cross-check the findings with other subcellular localization tools such as Cello, MetaLocGramN etc. [, ]. In this manuscript, a universal pipeline is proposed which could be applied on both the Gram positive and Gram negative bacteria in general; however, it is strongly suggested t […]

library_books

Light Regimes Shape Utilization of Extracellular Organic C and N in a Cyanobacterial Biofilm

2016
MBio
PMCID: 4937211
PMID: 27353754
DOI: 10.1128/mBio.00650-16

[…] of the 10 total replicates (5 biological and 2 technical for each treatment). We compared abundances of proteins between treatments using a Student’s t test. Localization predictions were made using MetaLocGramN () and SecretomeP () for nonclassical secretion prediction. CAZy enzymes were predicted using dbCAN (). […]

call_split

Salt Stress Induced Changes in the Exoproteome of the Halotolerant Bacterium Tistlia consotensis Deciphered by Proteogenomics

2015
PLoS One
PMCID: 4545795
PMID: 26287734
DOI: 10.1371/journal.pone.0135065
call_split See protocol

[…] in terms of sequence structure through inspection of the corresponding stop-to-stop open reading frame and blast results. The sequences obtained were exported into a FASTA file for evaluation by the MetaLocGramN facilities (http://genesilico.pl/MetaLocGramN/) [], SecretomeP 2.0 with settings for Gram-negative bacteria (http://www.cbs.dtu.dk/services/SecretomeP/) []and PRED-TAT (http://www.compgen […]

call_split

Proteomic Profiling of the Outer Membrane Fraction of the Obligate Intracellular Bacterial Pathogen Ehrlichia ruminantium

2015
PLoS One
PMCID: 4339577
PMID: 25710494
DOI: 10.1371/journal.pone.0116758
call_split See protocol

[…] TA format, was used for bioinformatics studies. The subcellular localization of the 948 E. ruminantium protein-coding genes was predicted using three global programs: PSORTb 3.0 [], CELLO 2.5 [], and MetaLocGramN []. The predicted utilization locations of each protein were filtered from raw software output using in-house scripts written in the R programming language and exported to Excel. In some […]

library_books

Combination of environmental stress and localization of l asparaginase in Arthrospira platensis for production improvement

2014
3 Biotech
PMCID: 4235887
PMID: 28324309
DOI: 10.1007/s13205-014-0215-z

[…] et al. ). The result of analysis was presented in supplementary material 1. The CELLO subcellular localization predictor system predicted that both ASNases were in the cytoplasmic area. Furthermore, MetaLocGramN analyses suggested that both ASNases were expressed in the cytoplasmic area with 65–85 % degrees of confidence. pSORTb predicted that both enzymes were in the cytoplasmic area and that ex […]

library_books

Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks

2013
BMC Genomics
PMCID: 3878776
PMID: 24330590
DOI: 10.1186/1471-2164-14-873

[…] ploaded from SEED [], UniProt [], and MicrobesOnline or extracted from the previous metabolic reconstruction of B. thetaiotaomicron[]. Predictions of cellular protein localization were obtained using MetaLocGramN []. […]

Citations

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MetaLocGramN institution(s)
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology Warsaw, Poland

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