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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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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 in pipelines

 (5)
2016
PMCID: 4914600
PMID: 27446006
DOI: 10.3389/fmicb.2016.00964

[…] 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 […]

2015
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 […]

2013
PMCID: 3806328
PMID: 23601235
DOI: 10.1111/1462-2920.12123

[…] rna genes were detected by using the rnammer 1.2 software () and transfer rnas by trnascan-se (). annotation was performed by using the gendb, version 2.2 system (), supplemented by the tool jcoast, version 1.6 (). for each predicted orf observations have been collected from similarity searches against sequence databases ncbi-nr, swiss-prot, kegg and genomesdb () and for protein family […]

2010
PMCID: 3815771
PMID: 21255355
DOI: 10.1111/j.1751-7915.2010.00183.x

[…] the genome of r. baltica was automatically re‐annotated based on updated homology searches [june 2005 – michanthi ()]. the updated annotation including all tool results are publicly available (). jcoast () was used as a tool for the visualization, interpretation, statistic (cog‐assignment) and comparison of genomic data stored in gendb v2.2 (). venn diagrams were generated by biovenn ()., […]

2009
PMCID: 2754498
PMID: 19725962
DOI: 10.1186/1471-2164-10-410

[…] of rhodopirellula baltica was automatically re-annotated based on updated homology searches (june 2005 - michanthi []). the updated annotation including all tool results is publicly available at []. jcoast [] was used as a tool for the visualization, interpretation, cog-assignment statistics and comparison of genomic data stored in gendb v2.2 []. the venn diagrams were generated by biovenn []., […]


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JCoast in publications

 (11)
PMCID: 4914600
PMID: 27446006
DOI: 10.3389/fmicb.2016.00964

[…] 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 […]

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 […]

PMCID: 4069401
PMID: 24522261
DOI: 10.1038/ismej.2014.4

[…] 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 […]

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

[…] (). the obtained hits were filtered based on a minimum e-value (1e−05) and an alignment length of 75% minimum, and 19% were found to be shared among the three communities ()., 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 […]

PMCID: 3738900
PMID: 23929484
DOI: 10.1128/genomeA.00594-13

[…] 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%. […]


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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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