Capri DNA page

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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).

Revision as of 17:22, 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 actions on a 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: add restriction enzyme sites to a given sequence
  • Shuffle: make mononucleotide shuffling of a given sequence

Search

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 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 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

Draw

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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