MACSIMS: User Guide


MACSIMS (Multiple Alignment of Complete Sequences Information Management System) is a multiple alignment-based information management system that combines the advantages of both knowledge-based and ab initio sequence analysis methods. Structural and functional information is mined automatically from the public databases. In the MACS, homologous regions are identified and the mined data is evaluated and propagated from known to unknown sequences with these reliable regions. MACSIMS provides a unique environment that facilitates knowledge extraction and the presentation of the most pertinent information to the biologist.

You can input an alignment in any of the most widely used formats, including MSF, FASTA and ClustalW. For sequences with Swissprot/TrEMBL identifiers, information is automatically mined from the public databases. The retrieved sequence features will be cross-validated and consistent features will be propagated from the characterised sequences to the uncharacterised ones. A number of ab initio predictions are also performed, including low complexity regions, coiled coil regions and transmembrane helices.

The processing may take a few minutes. You can either wait for the results to appear, or you can bookmark the page and come back to it later. Results wil be kept on the server for one week. You can retrieve previous results from the home page by entering the job ID number in the "Load previous session".

The MACSIMS results are displayed graphically using the JalView applet. The applet will allow you to view the alignment, select sequence features to be displayed, edit the alignmnet, build a phylogenetic tree, etc. You can also save the alignment in a number of different output formats.

MACSIMS validation and example alignments

MACSIMS has been validated in two large scale tests. All the alignments are available for viewing with JalView here :

BAliBASE tests

MS2PH tests

Sequence annotations provided by MACSIMS

MACSIMS takes advantage of the MAO Multiple Alignment Ontology to integrate the information mined from the public databases in the framewoek of the multiple alignment. The current ontology elements annotated by MACSIMS are:

MACS level annotations :

MAO element nameDescriptionData source
aln-namename of the MACSuser supplied
aln-scorequality score for the MACScalculated by NorMD in MACSIMS

Sequence level annotations :

MAO element nameDescriptionData source
seq-namesequence nameMACS
accessionsequence accession numberUniprot/PDB
nidsequence identifierUniprot/PDB
definitionsequence function definitionUniprot/PDB
goxrefGO cross-referenceUniprot
taxidNCBI taxidUniprot
taxonorganism lineageUniprot
hydrophobicitysequence mean hydrophobicitycalculated in MACSIMS

Sequence features :

Sequence features are associated with a specified segment of a sequence and are defined by their type, start and end positions, and a textual annotation.

Feature typeDescriptionData sourceFeature class
DOMAINstructural or functional domainUniprottext from Uniprot
PFAM-APfam structural or functional domainPfamPFnnnnn
PROSITEProsite domain or motif patternPrositePSnnnnn
STRUCTSecondary structure elementUniprot/PDBHELIX or STRAND
MODRESModified residueUniprottext from Uniprot
SITEActive siteUniprottext from Uniprot
VARSPLICSplicing variantUniprottext from Uniprot
VARIANTResidue variants or mutationsUniprottext from Uniprot
BLOCKConserved core blockcalculated in MACSIMSSBLOCK
REGIONHomologous regioncalculated in MACSIMSREGION
LOWCOMPLow complexity segmentcalculated in MACSIMSLOWC
TRANSMEMPotential transmembrane helixcalculated in MACSIMSTM
COILPotential coiled coilcalculated in MACSIMSCOIL

The feature class is prefixed by PROP_ if the information has been propagated from another sequence and the source sequence name is appended to the feature name.

The feature class is prefixed by PRED_ if the information has been predicted by an ab initio method in MACSIMS.