MACSIMS statistics

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Citations per year

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

This map represents all the scientific publications referring to MACSIMS per scientific context
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MACSIMS specifications

Information


Unique identifier OMICS_26387
Name MACSIMS
Alternative name Multiple Alignment of Complete Sequences Information Management System
Software type Toolkit/Suite
Interface Web user interface
Restrictions to use None
Input data Some multiple alignments.
Input format FASTA,MSF,ClustalW
Output data An alignment.
Output format XML
Computer skills Basic
Stability No
Maintained No
Wikipedia http://lbgi.fr/wikili/index.php/MACSIMS

Maintainers


This tool is not available anymore.

Additional information


http://www.lbgi.fr/~julie/MACSIMS/Documentation/

Information


Unique identifier OMICS_26387
Name MACSIMS
Alternative name Multiple Alignment of Complete Sequences Information Management System
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input data Some multiple alignments.
Input format FASTA,MSF,ClustalW
Output data An alignment.
Output format XML
Operating system Unix/Linux
Programming languages Shell (Bash)
Computer skills Advanced
Stability No
Requirements
SRS system, Secator, NCOILS
Maintained No
Wikipedia http://lbgi.fr/wikili/index.php/MACSIMS

Versioning


No version available

Maintainers


This tool is not available anymore.

Additional information


http://www.lbgi.fr/~julie/MACSIMS/Documentation/

Publication for Multiple Alignment of Complete Sequences Information Management System

MACSIMS citations

 (10)
library_books

MiSynPat: An integrated knowledge base linking clinical, genetic, and structural data for disease‐causing mutations in human mitochondrial aminoacyl‐tRNA synthetases

2017
Hum Mutat
PMCID: 5638098
PMID: 28608363
DOI: 10.1002/humu.23277

[…] lastic), then an underscore sign followed by 2 four letter codes for the Genus and species separated by a dot (e.g., Dmito_Homo.sapi stands for the human DARS2).Each alignment has been treated by the MACSIMS program (Thompson et al., ) in order to collect and propagate associated functional/structural features (PFAM‐A domains, PhyloBlock, secondary structures). We defined three conservation levels […]

library_books

The Chordate Proteome History Database

2012
Evol Bioinform Online
PMCID: 3418167
PMID: 22904610
DOI: 10.4137/EBO.S9186

[…] eriori, the most obvious artefacts. An artefact probability is supplied to the I.O.D.A user for all events. Our process detects two kind of artefacts:– Wrong propagation of domain architecture in the MACSIMS alignments (used to initiate our studies). The artefact detection agent re-predicts the apomorphic and plesiomorphic sequence domain architectures from the Pfam database to verify them.– Seque […]

library_books

KD4v: comprehensible knowledge discovery system for missense variant

2012
Nucleic Acids Res
PMCID: 3394327
PMID: 22641855
DOI: 10.1093/nar/gks474

[…] mapped to a 3D structure.The characterization of the background conservation and exploitation of the different types of evolutionary data has been described in detail previously (). Briefly, we used MACSIMS () to annotate a multiple alignment, containing both Uniprot and PDB sequences, with information such as: (i) taxonomic data, (ii) functional descriptions, (iii) known domains or domains simil […]

library_books

Controversies in modern evolutionary biology: the imperative for error detection and quality control

2012
BMC Genomics
PMCID: 3311146
PMID: 22217008
DOI: 10.1186/1471-2164-13-5

[…] program, since the computational speed of MAFFT is better suited to high throughput projects. The MSAs obtained from this pipeline were then annotated with structural and functional information using MACSIMS [], an information management system that combines knowledge-based methods with complementary ab initio sequence-based predictions. MACSIMS integrates several types of data in the alignment, i […]

library_books

Phylogeny of Galactolipid Synthase Homologs Together with their Enzymatic Analyses Revealed a Possible Origin and Divergence Time for Photosynthetic Membrane Biogenesis

2011
PMCID: 3276260
PMID: 22210603
DOI: 10.1093/dnares/dsr044

[…] nomic data at the Department of Energy Joint Genome Institute (DOE-JGI) website (www.jgi.doe.gov/). The resulting data are listed in Supplementary Table S1.MGD amino acid sequences were aligned using MACSIMS and MUSCLE, followed by a partial manual correction. To refine these data for phylogenetic analysis, the 5′- and 3′-terminal regions of MGD gene and regions where >15% of the species had a seq […]

library_books

EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data

2011
Evol Bioinform Online
PMCID: 3256995
PMID: 22267905
DOI: 10.4137/EBO.S8814

[…] ram, since the computational speed of MAFFT is better suited to high throughput projects. The MACS obtained from this pipeline were then annotated with structural and functional information thanks to MACSIMS, an information management system that combines knowledge-based methods with complementary ab initio sequence-based predictions. MACSIMS integrates several types of data in the alignment, in p […]


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MACSIMS institution(s)
Laboratoire de Biologie et Genomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; The Laboratory of Molecular Biology, Genetic Analysis & Modelling, Luxembourg; Post Genomics & Molecular Interactions Centre, School of Life Sciences, University of Dundee, UK
MACSIMS funding source(s)
Supported by the UK BBSRC (Biotechnology and Biological Sciences Research Council: BBS/B/16542), institute funds from the Institut National de la Santé et de la Recherche Medicale, the Centre National de la Recherche Scientifique, the Hopital Universitaire de Strasbourg, the Fond National de la Science (GENOPOLE) and the SPINE project (E.C. contract number QLG2-CT-2002-00988).

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