MACSIMS : multiple alignment of complete sequences information management system

BMC Bioinformatics

Table 1 feature propagation criteria

Feature type	Description	Data source	Feature category	Core block Coverage
DOMAIN	Structural/functional domain	Uniprot (predicted)	Domain	40%
PFAM-A	Pfam database domain	Pfam (reliable)	Domain	40%
PROSITE	Prosite motif or domain pattern	Prosite (predicted)	Single residue Domain	100% 40%
STRUCT	Secondary structure element	Uniprot/PDB (reliable)	SSE	70%
MODRES	Modified residue	Uniprot (predicted)	Single residue >1 residue	100% 70%
SITE	Active site	Uniprot (predicted)	Single residue >1 residue	100% 70%
VARSPLIC	Splicing variant	Uniprot (not propagated)	N/A	N/A
VARIANT	Residue variants or mutations	Uniprot (not propagated)	N/A	N/A
BLOCK	Conserved core block	Calculated in MACSIMS	N/A	N/A
REGION	Conserved region	Calculated in MACSIMS	N/A	N/A
LOWCOMP	Low complexity segment	Calculated in MACSIMS	N/A	N/A
TRANSMEM	Potential transmembrane helix	Calculated in MACSIMS	N/A	N/A
COIL	Potential coiled coil	Calculated in MACSIMS	N/A	N/A

The data source indicates the original database from which the feature type is retrieved (predicted indicates a feature type that may contain predicted/unreliable information; reliable indicates a feature type that is assumed to manually verified/reliable). The Feature category refers to the three categories used to determine the criteria for feature propagation. Core block coverage indicates the percentage of the feature that should be covered by core blocks for the feature to be propagated.

ISSN: 1471-2105