Capri DNA page

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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).

Revision as of 16:54, 20 June 2007

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.

Contents

Functions in single sequence analysis

Edit

Edit menu allows to manipulate a sequence or to display some informations

  • 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

Analyze menu allows to compute different sequence values

  • GC content: compute the GC percent
  • 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 [1]
  • 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[2]
  • 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).

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