CHROMA statistics

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Associated diseases

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CHROMA specifications

Information


Unique identifier OMICS_08915
Name CHROMA
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Windows
Computer skills Medium
Version 1.0
Stability Stable
Maintained Yes

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Publication for CHROMA

CHROMA in pipeline

2014
PMCID: 4235736
PMID: 25437606
DOI: 10.3390/pathogens3010025

[…] cutoff). the sam-format output files were converted to bam, sorted and indexed with samtools [] and displayed with artemis [,]. amino acid sequences were aligned with mafft [] and displayed with chroma []. the putative signal peptide region and tm segments highlighted in were predicted with signalp and psort [,,,]., pcr products spanning msp4 and the drhm gene (~680 bp and 390 bp, […]


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CHROMA in publications

 (14)
PMCID: 5869587
PMID: 29588502
DOI: 10.1038/s41598-018-23575-0

[…] visual inspection of multiple sequence alignments built using mafft version 7 (http://mafft.cbrc.jp/alignment/server/; ref.). for presentation purposes alignments were processed using the programme chroma (http://www.llew.org.uk/chroma/; ref.). phylogenetic analyses were carried out using multiple sequence alignments built with mafft and trimmed manually (with the aid of genedoc v2.7; […]

PMCID: 4535666
PMID: 26269100
DOI: 10.1186/s12859-015-0688-8

[…] by a plain blosum62 based algorithm are provided for comparison to demonstrate the difference between the new algorithm and a standard blosum matrix based algorithm. figure , annotated using chroma [], displays alignments for the glycosyltransferase domain provided to demonstrate the difference between the individual approaches and the coupled approach. the blosum-fire and blosum […]

PMCID: 4470819
PMID: 26083731
DOI: 10.1371/journal.pone.0128578

[…] functions. clustalw version 2.0 [] was used for sequence alignments and calculation of the percentage of identity between paired sequences. the consensus sequence of alignment was colored using chroma software []. the protein reported in this work is deposited in uniprot knowledgebase as entry c0hjm9 and nucleotide sequence is deposited in embl-ebi as entry ln606597., model construction […]

PMCID: 4072589
PMID: 24968201
DOI: 10.1371/journal.pone.0099394

[…] using microbesonline (http://www.microbesonline.org) . sequence alignments were made using clustalw (http://www.ebi.ac.uk/tools/clustalw2/index.html) . peptide alignments were annotated using chroma ., peptides were purchased from jpt peptide technologies (berlin, germany) at purity grades of 62–89%. transformation efficiencies might have been higher with highly pure peptides […]

PMCID: 4235736
PMID: 25437606
DOI: 10.3390/pathogens3010025

[…] cutoff). the sam-format output files were converted to bam, sorted and indexed with samtools [] and displayed with artemis [,]. amino acid sequences were aligned with mafft [] and displayed with chroma []. the putative signal peptide region and tm segments highlighted in were predicted with signalp and psort [,,,]., pcr products spanning msp4 and the drhm gene (~680 bp and 390 bp, […]


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CHROMA institution(s)
MRC Functional Genetics Unit, University of Oxford, Department of Human Anatomy and Genetics, Oxford, UK

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