Sequence formats

	The server can handle several file formats: plain text, Fasta, 
	NBRF/PIR and Swissprot format.

	Plain text format
		A sequence with one letter (small or capital) code
		(e.g. by copy and paste). This format can be applied 
		only for single sequence mode (see below).

		Example:

			ACFGHIKLMPQRTYVVFGHKLPPASSCVFGHKLMNVVVVDEQVREWTYPLLLASW
			ERTYMCDK
	Fasta format
		A sequence in FASTA format begins with a single-line description, 
		followed by lines of sequence data. The description line is 
		distinguished from the sequence data by a greater-than (">") 
		symbol in the first column. It is recommended that all lines 
		of the text should be shorter than 80 characters in length. 
		Sequences are expected to be represented in the standard 
		IUB/IUPAC amino acid codes. 
		
		Example:
			>MYPAT This is the name of my pat protein. In one line!
			TYPLKLPPASSCVFGHKLMNVVVVDEQVREWTYPLKLPPASSCVFGHKLMNVVVV
			DEQVREWTYPL
			>MYPATWO This is the name of my other pat protein. In one line!
			ACFGHIKLMPQRTYVVFGHKLPPASSCVFGHKLMNVVVVDEQVREWTYPLLLASW
			ERTYMCDKTYPLKLPPAS
	NBRF/PIR format
		A sequence in NBRF/PIR format begins with a two-line description, 
		followed by lines of sequence data. The description line is 
		distinguished from the sequence data by the starting symbols ">P1;".
		The second line contains the comments. The sequence have to end 
		by an asterisk ("*") symbol.
		
		Example:
			>P1;MYPAT 
			This is some comment in the second line.
			TYPLKLPPASSCVFGHKLMNVVVVDEQVREWTYPLKLPPASSCVFGHKLMNVVVV
			DEQVREWTYPL*
			>P1;MYPATWO 
			Hello it is just a comment.
			ACFGHIKLMPQRTYVVFGHKLPPASSCVFGHKLMNVVVVDEQVREWTYPLLLASW
			ERTYMCDKTYPLKLPPAS*

Sequence type

	The server can handle the submitted sequences by two different way:
	as single sequences or as homologue sequences.

	Single sequences
		The server sends back the topology prediction for each 
		sequence. For each prediction only the actual single 
		sequence information is used.
	Homologous sequences
		The server sends back only one topology prediction. All the 
		submitted sequences are used as homologues in the prediction. 
		The time of the prediction is linear for the number of 
		submitted sequences.


Prediction type
	The server can run in two different modes: as reliable or as fast.

	Reliable mode
		In this mode the server makes the Baum-Welch iteration 
		for the submitted sequence(s), i.e. it searches or makes 
		optimization for the best topology. Therefore the results 
		are reliable but this mode is more timeconsuming.
	Fast mode
		In this mode the server does not make the Baum-Welch 
		iteration for the submitted sequence(s), just does the 
		Viterbi algorithm using parameters derived from topology 
		information of wellknown transmembrane proteins. 
		Therefore, the results are generated very fast, but the 
		prediction accuracy is lower in this mode. This option is 
		useful for genome screening.

Localization of sequence part(s)

	If the localization of some parts of the query protein is known, then 
	this option allows to lock this or these part(s). The prediction will 
	be made using this restriction as conditional probabilities. The syntax 
	of the localisation is the following: begin_pos-end_pos-type, where 
	begin_pos and end_pos are the sequence numbers of the sequence piece 
	wanted to localise, while type is a one letter code of the cell parts, 
	where the sequence piece is localised (I: inside; i: inside-tail; H: 
	transmembrane-helix; O: outside; o: outside-tail).

	Examples:
		123-145-I		generates prediction where the sequence 
					piece between 123 and 145 will be in the 
					cytosol (inside).
		10-45-O 156-E-I		generates prediction where the sequence 
					pices between 10 and 45 will be outside 
					AND from the residue 156 to the C terminus 
					will be inside.

Output format

	The output can be generated as html file or as simple text file. The 
	last option is useful for additional processing of the result(s).

Results in one line

	Using this option results in a short output, where the prediction are
	in one line for each protein. The line begins with the >HP: symbol
	followed by the length and the name of the submitted protein, the 
	orientation of the first residue relative to the membrane (IN or OUT),
	then the number of the predicted transmembrane helices followed by the
	begin and end positions of the preditcted transmembrane helices.