MACSIMS: User Guide

Introduction

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 name	Description	Data source
aln-name	name of the MACS	user supplied
aln-score	quality score for the MACS	calculated by NorMD in MACSIMS

Sequence level annotations :

MAO element name	Description	Data source
seq-name	sequence name	MACS
accession	sequence accession number	Uniprot/PDB
nid	sequence identifier	Uniprot/PDB
definition	sequence function definition	Uniprot/PDB
goxref	GO cross-reference	Uniprot
organism	organism	Uniprot/PDB
taxid	NCBI taxid	Uniprot
taxon	organism lineage	Uniprot
hydrophobicity	sequence mean hydrophobicity	calculated 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 type	Description	Data source	Feature class
DOMAIN	structural or functional domain	Uniprot	text from Uniprot
PFAM-A	Pfam structural or functional domain	Pfam	PFnnnnn
PROSITE	Prosite domain or motif pattern	Prosite	PSnnnnn
STRUCT	Secondary structure element	Uniprot/PDB	HELIX or STRAND
MODRES	Modified residue	Uniprot	text from Uniprot
SITE	Active site	Uniprot	text from Uniprot
VARSPLIC	Splicing variant	Uniprot	text from Uniprot
VARIANT	Residue variants or mutations	Uniprot	text from Uniprot
BLOCK	Conserved core block	calculated in MACSIMS	SBLOCK
REGION	Homologous region	calculated in MACSIMS	REGION
LOWCOMP	Low complexity segment	calculated in MACSIMS	LOWC
TRANSMEM	Potential transmembrane helix	calculated in MACSIMS	TM
COIL	Potential coiled coil	calculated in MACSIMS	COIL

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.