CAPRI
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| - | CAPRI (Common Application Program Remote Interface) is a web interface for accessing all the major tools currently installed | + | 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== | ||
| - | [[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: | ||
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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. 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]] | ||
| - | More used functions in single sequence analysis divided for menu: | ||
| - | :''Analyze'': computing of GC content and 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. | ||
| - | More used 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). | ||
| === Protein Page === | === Protein Page === | ||
| - | Protein Page allows the analysis of proteic sequences. 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.]] | |
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| === Alignment Page === | === Alignment Page === | ||
| - | + | 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.]] | |
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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 | + | 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.]] |
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| - | + | === Tree Page === | |
| - | + | 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.]] | |
| - | === | + | |
| - | + | {{footer|footername=footer bioinfo}} | |
Current revision
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 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 here to access to CAPRI. Access is limited to registered users.
Contents |
[edit] Tool description
A page of CAPRI is a web-page consisting of:
- a text-area (1), in which user can insert and edit his data. For example, it is possible to paste directly one or more sequences in this area.
- a lateral menu bar (2), which allows to: open other pages, load data from disk, servers or databases, copy the visible data to a new page and select that sequences that have to be displayed.
- a top menu bar (3), which allows to access the installed analysis tool and which can dynamically changes depending on the number of data.
Clicking on a tool link in a menu, a new window appears showing all the modifiable options of such program and on the top-right a link to its documentation. Currently CAPRI implements five kinds of page to analyze five different biological data: DNA, protein, alignment, Hidden Markov Model (HMM) and phylogenetic tree; each page contains links to access to all the programs available for the analysis of respective input data. The result of each analysis is displayed in a new page, which type is in agreement with the output data: for example, DNA sequences are aligned within the 'DNA page' and the resulting alignment is provided in an 'alignment page'. Some tool provides more than one output. In this case the output page has a further button on the top-right corner which, once clicked, allows to switch to the other data.
[edit] 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. Go to functions
[edit] 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. Go to functions.
[edit] Alignment Page
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 here. Go to functions.
[edit] HMM Page
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. Go to functions.
[edit] Tree Page
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. Go to functions.
