MACSIMS statistics

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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

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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 in publications

 (5)
PMCID: 4021375
PMID: 24742296
DOI: 10.1186/1471-2105-15-111

[…] python scripts. the sm2ph knowledge base contains high quality multiple sequence alignments for all human proteins, which are annotated with structural and functional parameters derived from macsims (multiple alignment of complete sequences information management system). macsims combines knowledge-based methods with complementary ab initio sequence-based predictions to extract valuable […]

PMCID: 3418167
PMID: 22904610
DOI: 10.4137/EBO.S9186

[…] the retrieved data was integrated in the multiple alignment, together with a number of ab initio calculations (disordered regions, low-complexity segments and transmembrane helices), using the macsims information management system., based on the main figenix phylogeny pipeline, a new phylogeny pipeline was specifically developed to initiate phylogenetic studies from macsims alignment […]

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

[…] 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 […]

PMCID: 3202631
PMID: 21906678
DOI: 10.1016/j.ymeth.2011.08.014

[…] level of results integration for relatively few algorithms, but does not include display of results on a multiple sequence alignment (msa). greater integration over a user-supplied msa is offered by macsims which also propagates annotations by homology inference. however, macsims is not focused on structural biology and no ranking of sequences is given. also, macsims returns a limited subset […]

PMCID: 3018142
PMID: 21080938
DOI: 10.1186/1471-2164-11-634

[…] purposes. different views are available: (1) nucleic cdna sequence, (2) est trace and six-frame translation, (3) contig schematic representation, (4) consed-like [] contig alignment view, (5) macsims annotated protein alignment with customisable features display, (6) integrative view of the annotation process (text mining definition, ec number, gene ontology, pfam-a domains, kegg pathway […]


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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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