JCoast statistics

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Citations per year

Number of citations per year for the bioinformatics software tool JCoast
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Tool usage distribution map

This map represents all the scientific publications referring to JCoast per scientific context
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Associated diseases

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Popular tool citations

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Protocols

JCoast specifications

Information


Unique identifier OMICS_22810
Name JCoast
Alternative name Java Comparative Analysis and Search Tool
Software type Application/Script
Interface Graphical user interface, Application programming interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages Java
Database management system MySQL
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.7.b4
Stability Stable
Requirements
JRE, GenDB
Maintained Yes

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Versioning


No version available

Maintainers


  • person_outline Thierry Lombardot
  • person_outline Renzo Kottmann
  • person_outline Frank Oliver Glockner
  • person_outline Michael Richter

Publication for Java Comparative Analysis and Search Tool

JCoast citations

 (12)
library_books

Single cell Sequencing of Thiomargarita Reveals Genomic Flexibility for Adaptation to Dynamic Redox Conditions

2016
Front Microbiol
PMCID: 4914600
PMID: 27446006
DOI: 10.3389/fmicb.2016.00964

[…] nd transfer RNAs were identified with tRNAscan-SE (). The annotation was performed by a refined version of the GenDB v2.2 system () supplemented by the java-based comparative analysis and search tool JCoast version 1.7 (). Predicted ORFs were further verified via similarity searches against sequence databases NCBI-nr, Swiss-Prot, KEGG, COG, genomesDB (releases May 2013), and the protein family dat […]

library_books

Abundant toxin related genes in the genomes of beneficial symbionts from deep sea hydrothermal vent mussels

2015
eLife
PMCID: 4612132
PMID: 26371554
DOI: 10.7554/eLife.07966.025

[…] we used Glimmer () for open reading frame (ORF) prediction. Ribosomal RNA genes were detected with RNAmmer () and tRNAs with tRNAscan-SE (). Annotation was done with GenDB 2.4 () and supplemented by JCoast 1.7 () to integrate the results of BLASTp (cut-off e-value of 10.0) against sequence databases NCBI-nr () SwissProt (), KEGG (), COG (), Pfam (), and InterPro (). TMHMM () was used for transmem […]

call_split

Functional characterization of polysaccharide utilization loci in the marine Bacteroidetes ‘Gramella forsetii' KT0803

2014
PMCID: 4069401
PMID: 24522261
DOI: 10.1038/ismej.2014.4
call_split See protocol

[…] ned by means of the Geneious alignment software (). Details on protein functions were obtained from precomputed data available on the UniProt Knowledgebase (), the ENZYME database () and by using the JCoast software (). Information on the classification of CAZymes was derived from the CAZy database (). Subcellular localizations of all proteins were predicted according to ; the data are provided in […]

library_books

Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage

2014
PMCID: 4030236
PMID: 24430486
DOI: 10.1038/ismej.2013.242

[…] KEGG subsystem-based JCoast annotations were used to gain a better understanding of how these population shifts could influence their metabolic potential (). To extend this analysis, we compared the results with the Richm […]

call_split

Genome Sequence of Serratia plymuthica Strain S13, an Endophyte with Germination and Plant Growth Promoting Activity from the Flower of Styrian Oil Pumpkin

2013
Genome Announc
PMCID: 3738900
PMID: 23929484
DOI: 10.1128/genomeA.00594-13
call_split See protocol

[…] elding a final genome of 5,467,306 bp.Genes were identified with the software tool Prodigal 1/1/20 (). Functional annotation of the predicted genes was performed by use of the GenDB system 2.2 () and JCoast 1.7 (), which provided annotations with respect to clusters of orthologous groups (COG) (), Pfam (), and gene ontology (GO) (). The final genome includes 5.4 Mb, with a GC content of 56.19%. Th […]

call_split

Metabolic engineering of Bacillus subtilis for growth on overflow metabolites

2013
Microb Cell Fact
PMCID: 3728045
PMID: 23886069
DOI: 10.1186/1475-2859-12-72
call_split See protocol

[…] . subtilis 6051HGW []. In short, the GenBank file of B. licheniformis DSM13 [GenBank:AE017333] was imported into the GenDB 2.2 [] pipeline and the resulting database was used to analyze the ORFs with JCoast []. […]


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JCoast institution(s)
Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany, Jacobs University Bremen gGmbH, Bremen, Germany; Ribocon GmbH D-28359 Bremen, Germany
JCoast funding source(s)
Supported by the Max Planck Society.

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