Capri Alignment page

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	===Display===		===Display===
	Display menu allows to display sequence alignment features		Display menu allows to display sequence alignment features
-	:* Summary: display a sequence with selected features	+	:* Summary: give information on a multiple sequence alignments
-		+	:* Pretty: graphical display of aligned sequences with colouring and boxing
		+	:* Identities: display identical residues
		+	:* Similarities: display similar residues
		+	:* Dissimilarities: display dissimilar residues
		+	:* Non identities: display non identical residues
	===Analyze===		===Analyze===
-	Analyze menu allows to compute different sequence values	+	Analyze menu allows to compute different feature of sequence aligments
-		+	:* Consensus: compute the sequece consensus
-		+	:* Conservation: plot quality of conservation of a sequence alignment in a graphical mode
-	;Frequently used functions divided by menu:	+	:* Distance matrix: display a distance matrix
-	*''Display'': showing colored aligned sequences, identities and similarities.	+	:* Gapped matrix: display gapped matrix
-	*''Analyze'': analyzing consensus, distance matrix and computing an HMM.	+	:* Frequency matrix: display frequency matrix
		+	:* HMM: build an Hidden Markov Model.

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Revision as of 22:57, 20 June 2007

Alignment Page make available the analysis of nucleic or proteic sequence alignments. The only supported format is the MSF. It is possible to convert other alignment formats in MSF by clicking here.

Display

Display menu allows to display sequence alignment features

• Summary: give information on a multiple sequence alignments
• Pretty: graphical display of aligned sequences with colouring and boxing
• Identities: display identical residues
• Similarities: display similar residues
• Dissimilarities: display dissimilar residues
• Non identities: display non identical residues

Analyze

Analyze menu allows to compute different feature of sequence aligments

• Consensus: compute the sequece consensus
• Conservation: plot quality of conservation of a sequence alignment in a graphical mode
• Distance matrix: display a distance matrix
• Gapped matrix: display gapped matrix
• Frequency matrix: display frequency matrix
• HMM: build an Hidden Markov Model.