Capri DNA page - Revision history

Luca at 09:33, 21 June 2007

2007-06-21T09:33:31Z

←Older revision		Revision as of 09:33, 21 June 2007
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-	[[Image:Capri_dna_page.gif\|right]]
	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.
-		+	[[Image:Capri_dna_page.gif\|right]]
	==Functions in single sequence analysis==		==Functions in single sequence analysis==
	===Edit===		===Edit===

Luca at 09:32, 21 June 2007

2007-06-21T09:32:51Z

←Older revision		Revision as of 09:32, 21 June 2007
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-	[[Image:Capri_dna_page.gif]]	+	[[Image:Capri_dna_page.gif\|right]]
	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.

Luca at 09:32, 21 June 2007

2007-06-21T09:32:35Z

←Older revision		Revision as of 09:32, 21 June 2007
Line 1:		Line 1:
		+	[[Image:Capri_dna_page.gif]]
	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.

Luca: /* SearchDB */

2007-06-21T09:29:44Z

SearchDB

←Older revision		Revision as of 09:29, 21 June 2007
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	===SearchDB===		===SearchDB===
-	SearchDB menu ~~allow~~ to search in sequence databases which are currently installed at CEINGE. It is possible to search by using:	+	SearchDB menu allows to search in sequence databases which are currently installed at CEINGE. It is possible to search by using:
	:* Blast		:* Blast
	:* BlastX		:* BlastX

Luca: /* Search */

2007-06-20T17:19:06Z

←Older revision		Revision as of 17:19, 20 June 2007
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	:* Tandem repeats		:* Tandem repeats
	:* Inverted repeats		:* Inverted repeats
-	:* Pattern. Results can be displayed also in a graphical mode.	+	:* Pattern. Results can be displayed also in a graphical mode
-	:* ORFs (Open reading frames). Results can be displayed also in a graphical mode.	+	:* Matches from profile
		+	:* ORFs (Open reading frames). Results can be displayed also in a graphical mode
	:* Translated ORFs		:* Translated ORFs
	:* Protein pattern		:* Protein pattern
-	:* CpG islands. Results can be displayed also in a graphical mode.	+	:* CpG islands. Results can be displayed also in a graphical mode
	:* HLH binding sites.		:* HLH binding sites.
	:* TFsites (transcription factors)		:* TFsites (transcription factors)

Luca at 17:05, 20 June 2007

2007-06-20T17:05:41Z

←Older revision		Revision as of 17:05, 20 June 2007
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	Analyze menu allows to compute different sequence values		Analyze menu allows to compute different sequence values
	:* GC content: compute the GC percent		:* GC content: compute the GC percent
-	:* Words: ~~compute the~~ "words" ~~frequency; user can define the dimension of a word (~~in ~~nucleotides)~~	+	:* Words: count composition of "words" in a sequence
	:* Codon usage: chips calculates Nc statistic for the effective number of codons used [http://mac-web.ceinge.unina.it/bioinfo/public/pubprograms.php?action=read&displaymode=display&viewtype=form&id=15&nlines=1&language=en]		:* Codon usage: chips calculates Nc statistic for the effective number of codons used [http://mac-web.ceinge.unina.it/bioinfo/public/pubprograms.php?action=read&displaymode=display&viewtype=form&id=15&nlines=1&language=en]
	:* Tm profile: calculate DNA RNA/DNA melting temperature. There is also a graphical representation		:* Tm profile: calculate DNA RNA/DNA melting temperature. There is also a graphical representation

Luca at 15:31, 20 June 2007

2007-06-20T15:31:15Z

←Older revision		Revision as of 15:31, 20 June 2007
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	===SearchDB===		===SearchDB===
-	SearchDB allow to search in sequence databases which are currently installed at CEINGE. It is possible to search by using:	+	SearchDB menu allow to search in sequence databases which are currently installed at CEINGE. It is possible to search by using:
	:* Blast		:* Blast
	:* BlastX		:* BlastX
Line 64:		Line 64:
	==Functions in multi sequence analysis==		==Functions in multi sequence analysis==
	===Draw===		===Draw===
-	Draw ~~drawing a dot-~~plot, which ~~shows sequence~~ similarity between sequences	+	Draw menu allows to draw plot which are graphical representation of the regions of similarity between different sequences.
		+	:* DotPlot: quick comparison between different sequences
		+	:* WordDotPlot: comparison between different sequences based on defined windows
		+	:* DothPath: find the (nearly) optimal path aligning two sequences
		+
	===Search===		===Search===
-	~~searching matches~~ by profile	+	:* Matches by profile
	===Align===		===Align===
-	~~aligning~~ sequences with the most popular tools (ClustalW~~, matcher, strecher)~~.	+	Align menu allows to align sequences with the most popular tools like:
		+	:* Matcher
		+	:* Water
		+	:* Strecher
		+	:* Needle
		+	:* ClustalW
		+	:* to an HMM profile. The tool align sequences to an Hidden Markov Model profile.

Luca at 15:22, 20 June 2007

2007-06-20T15:22:32Z

←Older revision		Revision as of 15:22, 20 June 2007
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	===Process===		===Process===
-	Process menu allows to make some ~~action~~ on sequence	+	Process menu allows to make some actions on a sequence
	:* Reverse: give the reverse of a sequence		:* Reverse: give the reverse of a sequence
	:* Complement: give the reverse complement of a sequence		:* Complement: give the reverse complement of a sequence
	:* Mutagenise: simulate the mutation process of a given sequence[http://mac-web.ceinge.unina.it/bioinfo/public/pubprograms.php?action=read&displaymode=display&viewtype=form&id=88&nlines=1&language=en]		:* Mutagenise: simulate the mutation process of a given sequence[http://mac-web.ceinge.unina.it/bioinfo/public/pubprograms.php?action=read&displaymode=display&viewtype=form&id=88&nlines=1&language=en]
-	:* Add RE sites: ~~translate~~ a sequence ~~in protein~~	+	:* Add RE sites: add restriction enzyme sites to a given sequence
-	:* Shuffle: make mononucleotide shuffling of a given ~~sequences~~	+	:* Shuffle: make mononucleotide shuffling of a given sequence

-
-
-	making the complement and the translation in protein
	===Search===		===Search===
-	~~finding~~ restriction enzyme ~~(RE)~~ sites~~, patterns, open~~ reading frames (ORFs)~~, PCR primers and siRNAs~~	+	Search menu allows to find feature or particular entities in a given sequence. It is possible to search:
		+	:* RE sites (restriction enzyme sites)
		+	:* Palindrome
		+	:* Tandem repeats
		+	:* Inverted repeats
		+	:* Pattern. Results can be displayed also in a graphical mode.
		+	:* ORFs (Open reading frames). Results can be displayed also in a graphical mode.
		+	:* Translated ORFs
		+	:* Protein pattern
		+	:* CpG islands. Results can be displayed also in a graphical mode.
		+	:* HLH binding sites.
		+	:* TFsites (transcription factors)
		+	:* MAR/SAR (matrix/scaffold attachment regions)
		+	:* siRNA (silencing RNAs)
		+	:* Genes
		+	:* Gribskov plot: find genes by comparing codon usage with a codon frequency table
		+
	===Extract===		===Extract===
-	~~extracting a~~ sequence ~~fragment with the~~ given coordinates	+	Extract menu allows to extract portion of sequence from a given one.
		+	:* Fragment(s): extract fragments starting from input coordinates and give a number of sequences.
		+	:* Spliced fragments: extract fragments starting from input coordinates, which then were fused in a final sequence simulating a splicing process
		+	:* Segments: split the input sequence in a number of overlapping fragments.
		+
	===SearchDB===		===SearchDB===
-	~~searching~~ in sequence databases.	+	SearchDB allow to search in sequence databases which are currently installed at CEINGE. It is possible to search by using:
		+	:* Blast
		+	:* BlastX
		+	:* TBlastX

	==Functions in multi sequence analysis==		==Functions in multi sequence analysis==
	===Draw===		===Draw===
-	drawing a dot-plot, which shows sequence similarity between sequences	+	Draw drawing a dot-plot, which shows sequence similarity between sequences
	===Search===		===Search===
	searching matches by profile		searching matches by profile
	===Align===		===Align===
	aligning sequences with the most popular tools (ClustalW, matcher, strecher).		aligning sequences with the most popular tools (ClustalW, matcher, strecher).

Luca at 14:54, 20 June 2007

2007-06-20T14:54:24Z

←Older revision		Revision as of 14:54, 20 June 2007
Line 1:		Line 1:
	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.

-	;Functions in single sequence analysis	+	==Functions in single sequence analysis==
-	''Edit~~:''~~ allows to manipulate a sequence or to display some informations	+	===Edit===
-	:* Show: display a sequence with features, translation ~~and other informations.~~	+	Edit menu allows to manipulate a sequence or to display some informations
-	:* ~~reformatting~~	+	:* Show: display a sequence with selected features
		+	:* Show translated: display only translation
		+	:* Reformat: change the sequence format
		+	:* Insert: insert a sequence fragment in the given position
		+	:* Delete: delete a sequence fragment between the given coordinates
		+	:* Replace: replace a sequence fragment between the given coordinates with another chosen by the user
		+	:* Remove gaps: remove gaps from the sequence
		+	:* Trim ends: remove gaps and "n" only from the sequence ends

-	''Analyze:'' computing of
-	:* GC content
-	:* temperature melting
-	*''Process'': making the complement and the translation in protein
-	*''Search'': finding restriction enzyme (RE) sites, patterns, open reading frames (ORFs), PCR primers and siRNAs
-	*''Extract'': extracting a sequence fragment with the given coordinates
-	*''SearchDB'': searching in sequence databases.

-	;Functions in multi sequence analysis.	+	===Analyze===
-	*''Draw~~'':~~ drawing a dot-plot, which shows sequence similarity between sequences	+	Analyze menu allows to compute different sequence values
-	*''Search~~'':~~ searching matches by profile	+	:* GC content: compute the GC percent
-	*''Align~~'':~~ aligning sequences with the most popular tools (ClustalW, matcher, strecher).	+	:* Words: compute the "words" frequency; user can define the dimension of a word (in nucleotides)
		+	:* Codon usage: chips calculates Nc statistic for the effective number of codons used [http://mac-web.ceinge.unina.it/bioinfo/public/pubprograms.php?action=read&displaymode=display&viewtype=form&id=15&nlines=1&language=en]
		+	:* Tm profile: calculate DNA RNA/DNA melting temperature. There is also a graphical representation
		+	:* Twisting: calculate the number of turns of a double stranded DNA (or RNA) and other parameters
		+	:* Bending, Wobbling: display in a graphical view the calculated bending and wobbling of a sequence
		+	:* Isochore: plot isochores in large DNA sequences
		+
		+	===Process===
		+	Process menu allows to make some action on sequence
		+	:* Reverse: give the reverse of a sequence
		+	:* Complement: give the reverse complement of a sequence
		+	:* Mutagenise: simulate the mutation process of a given sequence[http://mac-web.ceinge.unina.it/bioinfo/public/pubprograms.php?action=read&displaymode=display&viewtype=form&id=88&nlines=1&language=en]
		+	:* Add RE sites: translate a sequence in protein
		+	:* Shuffle: make mononucleotide shuffling of a given sequences
		+
		+
		+
		+	making the complement and the translation in protein
		+	===Search===
		+	finding restriction enzyme (RE) sites, patterns, open reading frames (ORFs), PCR primers and siRNAs
		+	===Extract===
		+	extracting a sequence fragment with the given coordinates
		+	===SearchDB===
		+	searching in sequence databases.
		+
		+	==Functions in multi sequence analysis==
		+	===Draw===
		+	drawing a dot-plot, which shows sequence similarity between sequences
		+	===Search===
		+	searching matches by profile
		+	===Align===
		+	aligning sequences with the most popular tools (ClustalW, matcher, strecher).

Luca at 11:49, 20 June 2007

2007-06-20T11:49:19Z

←Older revision		Revision as of 11:49, 20 June 2007
Line 1:		Line 1:
	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.

-	;Functions in single sequence analysis.	+	;Functions in single sequence analysis
-	*''Analyze'': computing of GC content ~~and~~ temperature melting	+	''Edit:'' allows to manipulate a sequence or to display some informations
		+	:* Show: display a sequence with features, translation and other informations.
		+	:* reformatting
		+
		+	''Analyze:'' computing of
		+	:* GC content
		+	:* temperature melting
	*''Process'': making the complement and the translation in protein		*''Process'': making the complement and the translation in protein
	*''Search'': finding restriction enzyme (RE) sites, patterns, open reading frames (ORFs), PCR primers and siRNAs		*''Search'': finding restriction enzyme (RE) sites, patterns, open reading frames (ORFs), PCR primers and siRNAs