SEView classes

A few remarks

• To save space, only the non-obvious fields are described.
• Unless stated otherwise in the Description, all fields are alphanumeric strings, except for position, begin and end which are integers.
• Some symbols are variable, those represented below are only examples.
• Some inconsistencies might well persist :-) This is mostly for historical reasons, and also to keep compatibility with CGI scripts on other servers (such as ExPASy).

Protein features

Class Name	Symbol	Fields	Description
ActiveSite		position, comment	Residue that belongs to an enzyme's active site
DNABind		begin, end, comment	DNA binding domain
Domain		begin, end, comment	Generic, unlabeled domain
GlycSite		position, comment	Glycosylated residue
Helix		begin, end	Alpha helix
LabeledDomain		begin, end, comment, label	Generic domain with a user-supplied label. This class has specialized subclasses
Lipid		position, comment	Lipid-modified residue
MetalBind		position, comment, symbol	Residue with a metal ligand. symbol is the metal's chemical symbol.
ModRes		position, comment, type	Covalently modified residue. The type is a single letter denoting the modification type. Valid letters are P (phosphorylation), S (sulfatation), A (acetylation), H (hydroxylation), Y (pyrrolidone carboxylic acid), G (gamma-carboxylation), a (amidation), M (methylation).
Mutation		position, comment	Point mutation
Repeat		begin, end, comment	Repeated region
SSb		begin, end, comment	Intra-chain disulfide bridge
Strand		begin, end	Beta strand
Term		position, symbol, comment	Terminus. The type is denoted with the one-letter symbol, which can be N or C, but also for example S (start of signal peptide) or P (propeptide), etc. This is also used in DNA sequences for identifying 5' and 3' termini.
Transmem		begin, end, comment	Transmembrane domain
Turn		begin, end	Turn (in secondary structure)
Variant		position, comment	Sequence variant
Varsplic		begin, end, comment	Splicing variant
XSSb		begin, end, comment	Inter-chain disulfide bridge

DNA features

Class Name	Symbol	Fields	Description
BindingSite		begin, end, comment, URL	Protein binding site. URL is meant to point to a related document, for example in the TRANSFAC database
EMBLSequence		begin, end, comment, URL	This is used to represent EMBL (or any other DNA database) entries that are referencesd by the displayed data (cf EPD). The URL is intended to be a pointer to this entry on some server.
InitSite		position, name, URL	Transcription initiation site. name could be an EPD identifier, and URL a link to the corresponding EPD entry on some server

Predicted motifs

Class Name	Symbol	Fields	Description
HeightScaleDomain		begin, end, comment, label, URL, rel_score, type	The label is displayed on the symbol unless too wide. The URL can for example link to documentaion about the motif. The rel_score is a real number between 0 (worst score) and 1 (best core) and is reflected by the symbol's height. The type is an integer that is used to classify hits into groups (for example by database or domain type), and are reflected by the symbol's color.