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T3_MM specifications

Information


Unique identifier OMICS_09096
Name T3_MM
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Protein sequence(s)
Input format FASTA
Operating system Unix/Linux
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Aaron P. White <>

Information


Unique identifier OMICS_09096
Name T3_MM
Interface Web user interface
Restrictions to use None
Input data Protein sequence(s)
Input format FASTA
Programming languages R
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Aaron P. White <>

Publication for T3_MM

T3_MM in publications

 (6)
PMCID: 5054392
PMID: 27713481
DOI: 10.1038/srep34516

[…] without psi-blast hit). the combined method, peffect, outperformed both its components, reaching an f1 measure of 0.91 ()., we compared peffect to publicly available methods: bpbaac, effectivet3, t3_mm, modlab and bean 2.0. bpbaac, effectivet3, t3_mm and modlab focus exclusively on n-terminal features, while bean 2.0 and peffect are not confined to those regions only (methods, ). bpbaac, […]

PMCID: 4811931
PMID: 27065959
DOI: 10.3389/fmicb.2016.00387

[…] and maximum likelihood phylogenetic trees were reconstructed using raxml, with 100 bootstrap repetitions., a de-novo prediction of the effectors was performed using effectivet3 v1.0.1, bpbaac, and t3_mm (arnold et al., ; wang et al., , ). in order to minimize the number of false positives, we considered only the proteins predicted by all three tools. to this dataset were added proteins […]

PMCID: 4320434
PMID: 25518728
DOI: 10.1186/1471-2164-15-1135

[…] bacterial virulence [], we analyzed sequences in this genomic island to determine whether there is any t3ss secreted protein. using a combination of available t3ss prediction tools including t3_mm [], effective t4 [], and t3ss effector prediction [], we found that the third protein in this genomic island showed positive results in all of the prediction tools.table 3*amino acids., *amino […]

PMCID: 3931295
PMID: 24533538
DOI: 10.1186/1471-2180-14-40

[…] we compared the data from our t3s assays (including the controls, ct082, ct694, and rplj) with predictions of t3s substrates by in silico methods (effective t3s [], sieve [], modlab [], and t3_mm []) using resources available in the web (effective t3s, modlab and t3_mm) and table three in reference [] (sieve), as detailed in additional file : table s3. when considering the analysis […]

PMCID: 3617162
PMID: 23593149
DOI: 10.1371/journal.pone.0059754

[…] and amino acid composition of t3s signal regions while bpbaac only considers the amino acid composition features . compared with other software, such as sieve , effective t3 , sse-acc , t3_mm , etc., which mostly extracts the sequence-based features, the uniqueness of t3sepre is using position-specific instead of sequence-based features. because each of these software tools adopts […]


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T3_MM institution(s)
Genomics Research Center, Haerbin Medical University, Harbin, China; School of Life Science, the Chinese University of Hong Kong, Shatin, New Territories, Hong Kong; Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada

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