Capri Protein page

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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 changes if one, two or more sequences are inserted and analyzed at the same time, indicating which tools are available for the analysis. 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 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'': analysis of proteolytic enzyme or reagent cleavage digest, of charge, isoelectric point and secondary structure +===Edit===
-*''Process'': making the back-translation and the shuffling+Edit menu allows to manipulate a sequence or to display some informations
-*''Search'': searching pattern, coiled coil, transmembrane tract, cleavage and antigenic sites. +:* Reformat: change the sequence format
-*''Extract'': extracting a sequence fragment with the given coordinates +:* Insert: insert a sequence fragment in the given position
-*''SearchDB'': searching in sequence databases.+:* 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 "z" only from the sequence ends
-;Functions in multi sequence analysis. + 
-*''Draw'': drawing a dot-plot, which shows sequence similarity between sequences +===Analyze===
-*''Search'': searching matches by profile+Analyze menu allows to compute different sequence values
-*''SearchDB'': searching in sequence databases.+:* Digest: finds the positions where a specified proteolytic enzyme or reagent might cut a peptide sequence
-*''Align'': aligning sequences with the most popular tools (ClustalW, matcher, strecher) or to an HMM profile.+:* Words: count composition of "words" in a sequence
 +:* Charge: graphical view of the charges of the amino acids within a window of specified length
 +:* Isoelectric point: calculates the isoelectric point of a protein
 +:* Hydropathy: displays protein hydropathy
 +:* Hydroph moment: Hydrophobic moment calculation
 +:* Secondary structure: predicts protein secondary structure
 +:* Helical net: graphical display of proteins as a helical net
 +:* Helical wheel: graphical display of protein sequences as helices
 + 
 +===Process===
 +Process menu allows to make some actions on a sequence
 +:* Backtranslate: make the best estimate of the likely nucleic acid sequence the protein could have come from[http://mac-web.ceinge.unina.it/bioinfo/public/pubprograms.php?action=read&displaymode=display&viewtype=form&id=7&nlines=1&language=en]
 +:* 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:
 +:* Pattern. Results can be displayed also in a graphical mode.
 +:* Matches from profile
 +:* Prosite motifs (from the PROSITE motif database)sequence[http://mac-web.ceinge.unina.it/bioinfo/public/pubprograms.php?action=read&displaymode=display&viewtype=form&id=104&nlines=1&language=en]
 +:* Fingerprints (from PRINTS: a database of diagnostic protein signatures, or fingerprints.)
 +:* Coiledcoils
 +:* Cleavage sites
 +:* Transmembrane regions (graphical display)
 +:* Antigenic sites (graphical display)
 + 
 +===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 menu allow to search in sequence databases which are currently installed at CEINGE. It is possible to search by using:
 +:* Blast
 +:* PSIBlast
 +:* PFammHMM
 + 
 +==Functions in multi sequence analysis==
 +===Draw===
 +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===
 +:* Matches by profile
 +===SearchDB===
 +:* PfammHMM: search the Pfamm database by using an Hidden Markov Model.
 +===Align===
 +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.

Revision as of 19:32, 20 June 2007

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 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

  • 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 "z" only from the sequence ends


Analyze

Analyze menu allows to compute different sequence values

  • Digest: finds the positions where a specified proteolytic enzyme or reagent might cut a peptide sequence
  • Words: count composition of "words" in a sequence
  • Charge: graphical view of the charges of the amino acids within a window of specified length
  • Isoelectric point: calculates the isoelectric point of a protein
  • Hydropathy: displays protein hydropathy
  • Hydroph moment: Hydrophobic moment calculation
  • Secondary structure: predicts protein secondary structure
  • Helical net: graphical display of proteins as a helical net
  • Helical wheel: graphical display of protein sequences as helices

Process

Process menu allows to make some actions on a sequence

  • Backtranslate: make the best estimate of the likely nucleic acid sequence the protein could have come from[1]
  • 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:

  • Pattern. Results can be displayed also in a graphical mode.
  • Matches from profile
  • Prosite motifs (from the PROSITE motif database)sequence[2]
  • Fingerprints (from PRINTS: a database of diagnostic protein signatures, or fingerprints.)
  • Coiledcoils
  • Cleavage sites
  • Transmembrane regions (graphical display)
  • Antigenic sites (graphical display)

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 menu allow to search in sequence databases which are currently installed at CEINGE. It is possible to search by using:

  • Blast
  • PSIBlast
  • PFammHMM

Functions in multi sequence analysis

Draw

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

  • Matches by profile

SearchDB

  • PfammHMM: search the Pfamm database by using an Hidden Markov Model.

Align

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.
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