CHROMA statistics

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Citations per year

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

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

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Popular tool citations

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Protocols

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

Versioning


No version available

Publication for CHROMA

CHROMA citations

 (11)
library_books

Extensive molecular tinkering in the evolution of the membrane attachment mode of the Rheb GTPase

2018
Sci Rep
PMCID: 5869587
PMID: 29588502
DOI: 10.1038/s41598-018-23575-0

[…] y 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; http://gen […]

library_books

Robust sequence alignment using evolutionary rates coupled with an amino acid substitution matrix

2015
BMC Bioinformatics
PMCID: 4535666
PMID: 26269100
DOI: 10.1186/s12859-015-0688-8

[…] produced 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. FigureĀ , 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 alignmen […]

library_books

Control of Competence for DNA Transformation in Streptococcus suis by Genetically Transferable Pherotypes

2014
PLoS One
PMCID: 4072589
PMID: 24968201
DOI: 10.1371/journal.pone.0099394

[…] rformed 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 . […]

call_split

Comparative Genomics Identifies a Potential Marker of Human Virulent Anaplasma phagocytophilum

2014
PMCID: 4235736
PMID: 25437606
DOI: 10.3390/pathogens3010025
call_split See protocol

[…] tity 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 [,,,]. […]

library_books

Structure of the type IV secretion system in different strains of Anaplasma phagocytophilum

2012
BMC Genomics
PMCID: 3556328
PMID: 23190684
DOI: 10.1186/1471-2164-13-678

[…] when gap closure could not be completed due to such structures, as was the case with the extremely long virB6-4 R4 (Figure A) region.Amino acid sequences were aligned with MAFFT [] and displayed with CHROMA []. Taxonomic relationships used a neighbor-joining tree and the ITT substitution model [] and were displayed using Archaeopteryx (http://www.phylosoft.org/archaeopteryx). Hydrophobicity analys […]

library_books

A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems

2011
Nucleic Acids Res
PMCID: 3113570
PMID: 21306995
DOI: 10.1093/nar/gkr036

[…] , PROMALS (), KALIGN () and PCMA () programs, followed by manual adjustments on the basis of profileā€“profile and structural alignments. The consensus for alignments were calculated and colored by the Chroma program (). Secondary structures were predicted using the JPred and PSIPred programs (,). For earlier known domains the PFAM database () was used as a guide, though the profiles were often augm […]


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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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