LocDB statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

LocDB specifications

Information


Unique identifier OMICS_04487
Name LocDB
Restrictions to use None
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/LocDB

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana
  • Primates
    • Homo sapiens

Maintainer


  • person_outline Shruti Rastogi

Publication for LocDB

LocDB citations

 (10)
library_books

Inter genome comparison of the Quorn fungus Fusarium venenatum and the closely related plant infecting pathogen Fusarium graminearum

2018
BMC Genomics
PMCID: 5907747
PMID: 29673315
DOI: 10.1186/s12864-018-4612-2

[…] Interproscan-55.0 was used to identify signal and transmembrane domains. Proteins smaller than 20 amino acids were excluded. ProtComp (Version 9.0) (Softberry, USA) and result columns, LocDB and PotLocDB were used to exclude GPI anchored membrane proteins and other non-extracellular loci proteins. WoLfPSort [] (extracellular score > 17, WoLfPSort) was used to identify final destinat […]

library_books

Genome wide association analysis and QTL mapping reveal the genetic control of cadmium accumulation in maize leaf

2018
BMC Genomics
PMCID: 5785805
PMID: 29370753
DOI: 10.1186/s12864-017-4395-x

[…] n sub-cellular localization was predicted using ProtComp version 9 (http://linux1.softberry.com/berry.phtml) which compared homologous proteins of known localization and pentamer distributions in the LocDB and PotLocDB databases. […]

library_books

Draft whole genome sequence of groundnut stem rot fungus Athelia rolfsii revealing genetic architect of its pathogenicity and virulence

2017
Sci Rep
PMCID: 5509663
PMID: 28706242
DOI: 10.1038/s41598-017-05478-8

[…] rminal Signal peptides were enlisted. Further, the proteins obtained from both classical and non-classical pipeline were subjected to sub-cellular localization prediction using ProtComp v9.0 based on LocDB and PotLocDB databases (http://www.softberry.com). Finally, GPI-anchor proteins were filtered out from the final set and rest of the sequences were the designated as secretome. […]

library_books

Draft genome sequencing and secretome analysis of fungal phytopathogen Ascochyta rabiei provides insight into the necrotrophic effector repertoire

2016
Sci Rep
PMCID: 4835772
PMID: 27091329
DOI: 10.1038/srep24638

[…] in the N-terminal signal peptide were selected. Further, ProtComp v9.0 was employed to predict the localization of protein sequences obtained from both classical and non-classical pipeline, using the LocDB and PotLocDB databases Furthermore, the GPI-anchor proteins present in these extracellular predicted proteins were discarded. Finally, 538 proteins were predicted as classical secretory proteins […]

library_books

The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum

2015
BMC Genomics
PMCID: 4511438
PMID: 26198851
DOI: 10.1186/s12864-015-1756-1

[…] InterProscan-5.7-48.0 was used to identify signal and transmembrane domains. Proteins smaller than 20 amino acids were excluded. ProtComp (Version 9.0) [] and result columns, LocDB and PotLocDB were used to exclude GPI anchored membrane proteins and other non-extracellular loci proteins. WoLfPSort [] (extracellular score > 17, WoLfPSort) was used to identify final destinat […]

call_split

An Interspecies Comparative Analysis of the Predicted Secretomes of the Necrotrophic Plant Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

2015
PLoS One
PMCID: 4480369
PMID: 26107498
DOI: 10.1371/journal.pone.0130534
call_split See protocol

[…] were kept. GPI-anchor proteins were predicted by big-PI (http://mendel.imp.ac.at/gpi/cgi-bin/gpi_pred_fungi.cgi) []. ProtComp was also used to predict localisation of the remaining proteins using the LocDB and PotLocDB databases (ProtComp v8.0; http://www.softberry.com). WoLF PSORT analysis was done using ‘‘runWolfPsortSummaryfungi” in the WoLF PSORT v0.2 package, which estimates where proteins ar […]

Citations

Looking to check out a full list of citations?

LocDB institution(s)
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA

LocDB reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review LocDB