GDE Sequence Wrapper

Mapping of GDE file formats to GDE Sequence Wrapper

	value	GDE flat	GDE	GenBank
File extension		.flat	.gde	.gen, .gb, .gp
Name	non-blank string	first line	name	LOCUS
Accession	non-blank string		sequence-ID	ACCESSION
GI	integer			VERSION
Description	text		descrip	DESCRIPTION
Type	DNA\|RNA\|protein\|text\|mask	read from first character of each name line	type	LOCUS
Topology	linear\|circular	defaults to linear	circular [0\|1]	LOCUS
Annotation	text		comment	all lines from LOCUS to ORIGIN
Sequence	text	lines read after a name line, terminating with the next name line	sequence	read after the ORIGIN line and terminating with a "//" line.

Notes:

1. All files may contain 1 or more sequences.
2. We need to be able to read, write, and programmatically manipulate each of these fields. The latter means
that we need to be able to

enter this information as a "New Sequence"
cut, copy, paste
read values of these fields through the API ie. getters

GDE2.2 Manual
GenBank Release Notes
Sample GenPept protein entry: P13240