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ArchSchema specifications

Information


Unique identifier OMICS_21641
Name ArchSchema
Interface Web user interface
Restrictions to use None
Programming languages Java
Computer skills Basic
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Additional information


http://www.ebi.ac.uk/Tools/archschema/documentation.html

Information


Unique identifier OMICS_21641
Name ArchSchema
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability No
Requirements
JRE
Maintained No

Versioning


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Maintainer


This tool is not available anymore.

Additional information


http://www.ebi.ac.uk/Tools/archschema/documentation.html

Publication for ArchSchema

ArchSchema in pipeline

2012
PMCID: 3291543
PMID: 22396634
DOI: 10.1371/journal.pcbi.1002403

[…] to constitute a domain are checked against pfam and if a non-overlapping pfam domain is found then it is included in the mda. sequences with the same multi-domain architectures are clustered using archschema . the sequences of each cluster are then aligned using mafft , and the alignment used to perform the phylogenetic analysis., some superfamilies can have an extremely large number (tens […]


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ArchSchema in publications

 (3)
PMCID: 3855486
PMID: 24340054
DOI: 10.1371/journal.pone.0082705

[…] activity [], whereas 3kbq has been recently described as a new class of pyrophosphatase (eggnog code: cog1058) []. when the structure of a. tumefaciens cina (2a9s) was studied in detail using archschema [], a tool for interactive graphing of related pfam domain architectures, three well-defined groups could be identified attending to domain composition (). the first covers enzymes […]

PMCID: 3531114
PMID: 23203873
DOI: 10.1093/nar/gks1211

[…] to resources established at the european bioinformatics institute (ebi) (section f) that display information on the different multi-domain contexts in which this domain superfamily is observed [archschema section (f), ]. section (g), provides a link to the funtree () resource displaying phylogenetic information for enzyme superfamilies in cath. funtree is the product of a collaboration […]

PMCID: 3291543
PMID: 22396634
DOI: 10.1371/journal.pcbi.1002403

[…] . to explore how the addition of domains can affect a given domain's function, a different sub-clustering of the superfamily was made based on the unique multi-domain architecture identified using archschema . proteins that contain the superfamily domains in the same order are clustered together. these clusters are termed multi-domain architecture (mda) groups., we used macie , a manually […]


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ArchSchema institution(s)
Division of Mathematical Biology, The National Institute for Medical Research, The Ridgeway, Mill Hill, London, UK; European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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