Pipviewer is a visualizer for multiple alignements of genomic sequences. It highlights conserved regions and allows basic anotations. Its main goal is to find conserved probes for the construction of gene order data sets. Selected regions marked as probes can be expoxted to fasta format. It can also retreive gene annotations form the NBCI and display this information along the alignement.
Pipviewer is not an aligner. You must compute the alignment with another tool like Clustal or Multi PIP Maker.
Pipviewer is a Free Software released under the GNU GPL version 3. See COPYING.txt for the details.
The main window is composed of five parts:
the conservation viewer (top);
the text viewer (middle);
the actions panel (lower left);
the options panels and the informations panels (lower right).
The conservation viewer displays the conserved regions of the multiple alignment by using different colors zones and a curve representation. Gene annotations, when available, will show in the conservation viewer area.
The conservation plots are represented by colors zones, going from poorly to highly conserved region:
green/black represents a highly conserved region;
yellow/grey represents a moderate conserved region;
red/white represents a poorly conserved region or a gap.
The color view is more efficient when looking at a large segment of the alignment while the curve gives the detail of the conservation. The gray scale view if provided for color blind users.
The conservation curve represents the conservation zones by going up (highly conserved) or down (poorly conserved).
The gene annotations represent the genes found on the reference sequence:
genes found on the positive strand (Direct) are shown as green rectangles;
genes found on the negative strand are shown as purple rectangles.
The text viewer displays the base pairs details of a selected region. To select a region, drag the mouse across the conservation viewer. Selected regions are represented by blue rectangles. In the text view, notice that:
the reference sequence is always on top;
conserved nucleotides are shown as dots (.);
non-conserved nucleotides are shown as letters;
gaps are shown as dashes (-).
The actions panel provides multiples actions to the user:
probe: set a selected region as a "probe";
break point: set a selected region as a "break point";
trash: set a selected region as "trash";
check score: obtain informations about the quality of the selected region in term of alignment score;
skip: unselect a selection;
reset: reset a highlighted region.
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Note
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Typical usage is: - probes represent highly conserved region; - break points represent poorly conserved region; - trash should represents a region of no interest. |
The options panel displays the conservation viewer size (in nucleotides) with a spin-box; this is fully adjustable depending on whether you looking for and overview or a detailed view.
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Warning
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The conservation viewer uses OpenGL for renderering; setting the size of the viewer higher then 10000 without a 3D video card can result in serious slowdown. |
The informations panels provides multiples informations about the region selected :
Give informations about the length, the starting and the ending position of a selected region on the unaligned reference sequence/genome.
Give informations about the length, the starting and the ending position of a selected region on the aligned reference sequence/genome.
Give the number of probes the user has sets on the conservation viewer.
The species association window shows the number of species, the species's names and the accession number of their sequence database on the NCBI website.
Note:
Users can easily associate the accession number of the align sequence by double-clicking the sequence/specie/genome in the list.
The score window show the sequence names (target), the percentage of identities and the percentage of length of a selected region on the align reference sequence.
The probe list window shows the list of probe set by the user on the conservation viewer. Each probe possess its own name, starting and endind position, and length.
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Note
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Users can easily locate probes on the conservation viewer by double-clicking on the probes in the list. This can greatly accelerate the search for a specific probe. |
PipViewer can import multiple alignment from PipMaker http://pipmaker.bx.psu.edu/pipmaker and from ClustalW http://www.ebi.ac.uk/clustalw.
Multiple alignment file can be import using the Import option.
Imported files can be saved in the PipViewer format (.psel) using the save or save as options.
Saved files can be opened by using the open option.
PipViewer can take 2 .psel files and merge their data to obtain one.
Files can be merge using the Merge option.
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Important
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Files can only be merged if their sequence names and content are identical. |
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Warning
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Merging files can result in errors if some highlighted region set by the user intersect with each others. |
DNA sequence of the probes regions sets by the user can be exported to FASTA file using the Export Probes option.
Suffix can also be added to probes exported (optionel).
The genes annotations can be shown on the conservation viewer by selecting the Show Genes Annotations option.
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Note
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This option is only available if the user as performed an automated search of the genes annotations using the Compute Genes Annotations located in the Tools menu or if the annotations have been saved in the .psel file. |
The probes sets by the user can be shown via the Probes List.. option.
Accession numbers of each original sequence can be added to the corresponding align sequence using the Associate Accession Numbers option.
Setting accession number are performed by double-cliking the mouse over the selected sequence/species/genome and entering the code inside the dialog box.
Genes annotations can be compute by selecting Compute Genes Annotations.