CAPRI - Revision history

Leandra at 11:02, 22 June 2007

Leandra — Fri, 22 Jun 2007 11:02:08 GMT

←Older revision		Revision as of 11:02, 22 June 2007
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-	CAPRI (Common Application Program Remote Interface) is a web interface for accessing all the major tools currently installed ~~at CEINGE~~. ~~It was developed at CEINGE [[The bioinformatics group\|bionformatics lab]] and can be used only by registered users.~~	+	CAPRI (Common Application Program Remote Interface) is a web interface for accessing all the major tools currently installed on the bioinformatic site. CAPRI project was born to guarantee the researchers an easy access to many widely used sequence analysis tools, such as [[BLAST]], [[FastA]] or even packages like [[EMBOSS]], which were originally developed on a command line interface. It was originally developed by A. Davassi and M. Petrillo, within the lab, and has been subsequently adapted and mantained by the other people in the group.
-	CAPRI project was born to guarantee the researchers an easy access to many widely used sequence analysis tools, such as [[BLAST]], [[FastA]] or even packages like [[EMBOSS]], which were originally developed on a command line interface.	+
	CAPRI resembles a typical local desktop application where the user selects the sequences and uses a number of menus to access the various functions but, in reality, it takes advantage of the processing power and the databases available on the CEINGE's remote servers. Unlike other similar tools CAPRI does not require to install any software.		CAPRI resembles a typical local desktop application where the user selects the sequences and uses a number of menus to access the various functions but, in reality, it takes advantage of the processing power and the databases available on the CEINGE's remote servers. Unlike other similar tools CAPRI does not require to install any software.
-	Click [http://bioinfo.ceinge.unina.it/tools/winterf/capri/capri1.php here] to access to CAPRI.	+	Click [http://bioinfo.ceinge.unina.it/tools/winterf/capri/capri1.php here] to access to CAPRI. Access is limited to registered users.

	==Tool description==		==Tool description==
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	=== Alignment Page ===		=== Alignment Page ===
-	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 [http://bioinfo.ceinge.unina.it/tools/winterf/sreformat.php here]. [[Capri_Alignment_page\|Go to functions.]]	+	Alignment Page may be used to analyse nucleic or proteic sequence alignments. The basic supported format is the MSF. It is possible to convert other alignment formats to MSF by clicking [http://bioinfo.ceinge.unina.it/tools/winterf/sreformat.php here]. [[Capri_Alignment_page\|Go to functions.]]

	=== HMM Page ===		=== HMM Page ===
-	HMM page allows the analysis of Hidden Markov Models. HMM is a position-specific scoring system suitable for searching databases ~~for remotely homologous sequences which is~~ derived from the analysis of a multiple sequence ~~alignment. User cannot past data in directly in this page but can upload data from a file~~. [[Capri_HMM_page\|Go to functions.]]	+	HMM page allows the analysis of Hidden Markov Models. HMM is a position-specific scoring system, suitable for searching databases with patterns derived from the analysis of multiple sequence alignments. [[Capri_HMM_page\|Go to functions.]]

	=== Tree Page ===		=== Tree Page ===
-	Tree page allows the analysis of ~~phylogenetic~~ trees. It plots a rooted or unrooted tree diagram, with the possibility of orientation of tree and branches, label sizes and angles, margin sizes.	+	Tree page allows the analysis of trees such as those used in phylogenetic analyses. It plots a rooted or unrooted tree diagram, with the possibility of orientation of tree and branches, label sizes and angles, margin sizes.
	[[Capri_Tree_page\|Go to functions.]]		[[Capri_Tree_page\|Go to functions.]]

	{{footer\|footername=footer bioinfo}}		{{footer\|footername=footer bioinfo}}

Giovanni at 06:48, 22 June 2007

Giovanni — Fri, 22 Jun 2007 06:48:07 GMT

←Older revision		Revision as of 06:48, 22 June 2007
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	[[Capri_Tree_page\|Go to functions.]]		[[Capri_Tree_page\|Go to functions.]]

-	{{footer bioinfo}}	+	{{footer\|footername=footer bioinfo}}

Giovanni at 15:51, 20 June 2007

Giovanni — Wed, 20 Jun 2007 15:51:55 GMT

←Older revision		Revision as of 15:51, 20 June 2007
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	Tree page allows the analysis of phylogenetic trees. It plots a rooted or unrooted tree diagram, with the possibility of orientation of tree and branches, label sizes and angles, margin sizes.		Tree page allows the analysis of phylogenetic trees. It plots a rooted or unrooted tree diagram, with the possibility of orientation of tree and branches, label sizes and angles, margin sizes.
	[[Capri_Tree_page\|Go to functions.]]		[[Capri_Tree_page\|Go to functions.]]
		+
		+	{{footer bioinfo}}

Luca: /* Tool description */

Luca — Wed, 20 Jun 2007 15:16:43 GMT

Tool description

←Older revision		Revision as of 15:16, 20 June 2007
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	==Tool description==		==Tool description==
-	[[Image:Capri_home.jpg\|right\|500px\|Capri home page]]	+	[[Image:Capri_home.jpg\|right\|thumb\|500px\|Capri home page]]

	A page of CAPRI is a web-page consisting of:		A page of CAPRI is a web-page consisting of:

Luca at 11:33, 20 June 2007

Luca — Wed, 20 Jun 2007 11:33:58 GMT

←Older revision		Revision as of 11:33, 20 June 2007
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	HMM page allows the analysis of Hidden Markov Models. HMM is a position-specific scoring system suitable for searching databases for remotely homologous sequences which is derived from the analysis of a multiple sequence alignment. User cannot past data in directly in this page but can upload data from a file. [[Capri_HMM_page\|Go to functions.]]		HMM page allows the analysis of Hidden Markov Models. HMM is a position-specific scoring system suitable for searching databases for remotely homologous sequences which is derived from the analysis of a multiple sequence alignment. User cannot past data in directly in this page but can upload data from a file. [[Capri_HMM_page\|Go to functions.]]

-	=== ~~TREE~~ Page ===	+	=== Tree Page ===
-	~~TREE~~ page allows the analysis of phylogenetic trees. It plots a rooted or unrooted tree diagram, with the possibility of orientation of tree and branches, label sizes and angles, margin sizes.	+	Tree page allows the analysis of phylogenetic trees. It plots a rooted or unrooted tree diagram, with the possibility of orientation of tree and branches, label sizes and angles, margin sizes.
		+	[[Capri_Tree_page\|Go to functions.]]

Luca at 11:27, 20 June 2007

Luca — Wed, 20 Jun 2007 11:27:02 GMT

←Older revision		Revision as of 11:27, 20 June 2007
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	=== DNA Page ===		=== DNA Page ===
	DNA page is the CAPRI default page that allows to analyze nucleic acid sequences like DNA or RNA. User can edit, translate or align its sequences or search within the installed databases. Top menu bar changes if one, two or more sequences are inserted and analyzed at the same time, indicating which tools are available for the analysis.		DNA page is the CAPRI default page that allows to analyze nucleic acid sequences like DNA or RNA. User can edit, translate or align its sequences or search within the installed databases. Top menu bar changes if one, two or more sequences are inserted and analyzed at the same time, indicating which tools are available for the analysis.
-	[[Capri_DNA_page\|Go to functions~~...~~]]	+	[[Capri_DNA_page\|Go to functions]]

	=== Protein Page ===		=== Protein Page ===
	Protein Page allows the analysis of proteic sequences. User can edit, back-translate or align its sequences or search within the installed databases. Top menu bar behaviour is similar to the DNA page.		Protein Page allows the analysis of proteic sequences. User can edit, back-translate or align its sequences or search within the installed databases. Top menu bar behaviour is similar to the DNA page.
-	[[Capri_Protein_page\|Go to functions...]]	+	[[Capri_Protein_page\|Go to functions.]]

	=== Alignment Page ===		=== Alignment Page ===
-	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 [http://bioinfo.ceinge.unina.it/tools/winterf/sreformat.php here]. [[Capri_Alignment_page\|Go to functions...]]	+	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 [http://bioinfo.ceinge.unina.it/tools/winterf/sreformat.php here]. [[Capri_Alignment_page\|Go to functions.]]

	=== HMM Page ===		=== HMM Page ===
	HMM page allows the analysis of Hidden Markov Models. HMM is a position-specific scoring system suitable for searching databases for remotely homologous sequences which is derived from the analysis of a multiple sequence alignment. User cannot past data in directly in this page but can upload data from a file. [[Capri_HMM_page\|Go to functions.]]		HMM page allows the analysis of Hidden Markov Models. HMM is a position-specific scoring system suitable for searching databases for remotely homologous sequences which is derived from the analysis of a multiple sequence alignment. User cannot past data in directly in this page but can upload data from a file. [[Capri_HMM_page\|Go to functions.]]
-	More used functions divided for menu:
-	:''Aling'': aligning sequences to the HMM.
-	:''Extract'': extracting consensus or a number of sequences in agreement with the HMM.
-	:''SearchDB'': searching databases with the HMM.

	=== TREE Page ===		=== TREE Page ===
	TREE page allows the analysis of phylogenetic trees. It plots a rooted or unrooted tree diagram, with the possibility of orientation of tree and branches, label sizes and angles, margin sizes.		TREE page allows the analysis of phylogenetic trees. It plots a rooted or unrooted tree diagram, with the possibility of orientation of tree and branches, label sizes and angles, margin sizes.

Luca: /* HMM Page */

Luca — Wed, 20 Jun 2007 11:26:11 GMT

HMM Page

←Older revision		Revision as of 11:26, 20 June 2007
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	=== HMM Page ===		=== HMM Page ===
-	HMM page allows the analysis of Hidden Markov Models. HMM is a position-specific scoring system suitable for searching databases for remotely homologous sequences which is derived from the analysis of a multiple sequence alignment. User cannot past data in directly in this page~~, he~~ can ~~only~~ upload data from file.	+	HMM page allows the analysis of Hidden Markov Models. HMM is a position-specific scoring system suitable for searching databases for remotely homologous sequences which is derived from the analysis of a multiple sequence alignment. User cannot past data in directly in this page but can upload data from a file. [[Capri_HMM_page\|Go to functions.]]
	More used functions divided for menu:		More used functions divided for menu:
	:''Aling'': aligning sequences to the HMM.		:''Aling'': aligning sequences to the HMM.

Luca: /* Alignment Page */

Luca — Wed, 20 Jun 2007 11:20:45 GMT

Alignment Page

←Older revision		Revision as of 11:20, 20 June 2007
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	=== Alignment Page ===		=== Alignment Page ===
-	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 [http://bioinfo.ceinge.unina.it/tools/winterf/sreformat.php here]. [[ Capri_Alignment_page Go to functions...]]	+	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 [http://bioinfo.ceinge.unina.it/tools/winterf/sreformat.php here]. [[Capri_Alignment_page\|Go to functions...]]

	=== HMM Page ===		=== HMM Page ===

Luca: /* Alignment Page */

Luca — Wed, 20 Jun 2007 11:14:15 GMT

Alignment Page

←Older revision		Revision as of 11:14, 20 June 2007
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	=== Alignment Page ===		=== Alignment Page ===
-	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 [http://bioinfo.ceinge.unina.it/tools/winterf/sreformat.php here].	+	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 [http://bioinfo.ceinge.unina.it/tools/winterf/sreformat.php here]. [[ Capri_Alignment_page Go to functions...]]

	=== HMM Page ===		=== HMM Page ===

Luca: /* Alignment Page */

Luca — Wed, 20 Jun 2007 11:10:08 GMT

Alignment Page

←Older revision		Revision as of 11:10, 20 June 2007
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	=== Alignment Page ===		=== Alignment Page ===
-	~~With this page it~~ is possible to ~~analyze sequence alignments.~~	+	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 [http://bioinfo.ceinge.unina.it/tools/winterf/sreformat.php here].
-	~~More used functions divided for menu:~~	+
-	~~:''Display''~~: ~~showing colored aligned sequences, identities and similarities~~.	+
-	~~:''Analyze'': analyzing consensus, distance matrix and computing an HMM.~~	+
	=== HMM Page ===		=== HMM Page ===
	HMM page allows the analysis of Hidden Markov Models. HMM is a position-specific scoring system suitable for searching databases for remotely homologous sequences which is derived from the analysis of a multiple sequence alignment. User cannot past data in directly in this page, he can only upload data from file.		HMM page allows the analysis of Hidden Markov Models. HMM is a position-specific scoring system suitable for searching databases for remotely homologous sequences which is derived from the analysis of a multiple sequence alignment. User cannot past data in directly in this page, he can only upload data from file.