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LocTree specifications

Information


Unique identifier OMICS_04483
Name LocTree
Interface Web user interface
Restrictions to use None
Input format FASTA
Computer skills Basic
Version 3.0
Stability Stable
Maintained Yes

Information


Unique identifier OMICS_04483
Name LocTree
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes

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Publications for LocTree

LocTree in publications

 (75)
PMCID: 5924525
PMID: 29597290
DOI: 10.3390/genes9040183

[…] significance for each tree node was determined by bootstrap analysis using 100 replicates []., the subcellular localization was analyzed in silico using bacello [], eslpred [], yloc [], psort ii [], loctree3 [], wolf psort [], plant-mploc [], and cello []. the ncbi database was used to retrieve a 1500-bp dna sequence from the 5′-upstream region of each alba gene, and the corresponding cis-acting […]

PMCID: 5828069
PMID: 29482619
DOI: 10.1186/s13073-018-0521-x

[…] transcript was based on data and groupings from belland et al. []. predicted localization of expressed proteins was defined using the consensus from three predictions using cello [], psortb [] and loctree3 []., a permutation-based ordinal logistic regression model was used to test the association between the disease severity score (using the in vivo conjunctival phenotype defined previously) […]

PMCID: 5764023
PMID: 29320982
DOI: 10.1186/s12864-017-4425-8

[…] family. of the encoding proteins, 341 oscyps were predicted to be located on er, 11 on chloroplast (oscyp701as and oscyp74s) and three on mitochondrion (oscyp51h7p, oscyp711a2 and cyp727a1) by loctree3. all the related information was summarized in additional file : table s1. in addition to the subcellular localization prediction, conserved motif analysis is one of the important methods […]

PMCID: 5814146
PMID: 29447110
DOI: 10.7554/eLife.33322.026

[…] biological replicate, ) were generated using venn diagram plotter (ver. 1.5.5228.29250; pnnl). sub-cellular localization of proteins identified in ≥2 biological replicates () was predicted using the loctree3 database (ver. 23-08-2016; )., non-normalized protein intensities (non-lfq) were log2 transformed and averaged across replicates to assess differences in overall protein abundances (, ). lfq […]

PMCID: 5732408
PMID: 29312156
DOI: 10.3389/fmicb.2017.02394

[…] pst-78 predicted secretome was submitted to program effectorp with default parameters (sperschneider et al., )., the pst-78 predicted secretome was annotated using blast2go v3.3 (conesa et al., ). loctree3 (goldberg et al., ), and nucpred (brameier et al., ) were used to predict subcellular localizations. nlstradamus (nguyen et al., ) was used to predict nuclear localization signals. pfam […]


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LocTree institution(s)
TUM, Bioinformatik-I12, Informatik, Garching, Germany

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