VIGS Running
Modify parameters help
- The best target region score value indicates how good the yellow highlighted region is, taking into account the number of target and off-target n-mers. The closer to 100 the better is the value. In the same way, the custom region score indicates the value of the custom region, represented by the transparent grey rectangle.
- Set Custom Region button will activate a draggable and resizable transparent grey rectangle to manually select a custom region.
- Change button will recalculate the results using the new parameters chosen. Changing the n-mer size is the slowest step.
Distribution of n-mers help
- N-mers mapping to the target/s are shown in blue and to off-targets in red. The yellow area highlights the region with the highest score using the selected parameters
- The bottom graph represents in red the score values along the sequence. The score value = 0 is indicated with a green line. Below this line are represented the regions with more off-targets than targets, and the opposite when the score is above the green line.
- Expand graph button will display every n-mer fragment aligned over the query for each subject.
- Zoom button will zoom in/out the VIGS map representation.
Best region help
- This section shows the best or the custom region sequence in FASTA format.
- The custom region will update as the grey selection rectangle is moved.
Sequence overview help
- In this section is shown the query sequence, highlighting the best target region in yellow or the custom region in grey.
- The custom region will be updated as the grey selection rectangle is moved.
Description of genes mapped help
- Number of n-mer matches and gene functional description are shown for each matched gene.
- The View link will open a draggable dialog with this information.
Parameters used
Usage Help
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1. Paste a sequence like in one of the examples:
>gene_ID ATGGATCAGTCGGTGTTGGCGATCT ACAGCTTGGCCAACTCCAGAAATTGATGGATCAGTCGGTGTTGGCGATCTSolyc10g047140.1.1 -
2. Choose n-mer size, nucleotide stretch size in bp, used to identify targeted regions (18-24, Default=21)
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3. Choose Fragment length, desired VIGS fragment length in bp (100-Sequence length, Default=300)
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4. Choose mismatches, number of mismatches allowed in the alignment (0-2, Default=0)
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5. Choose database
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6. Upload a expression values file (optional). It must be a tab delimited text file, with gene identifiers in the first column and a header in the first row:
gene_id expr_val p_val ... Solyc10g047140.1.1 4.56 0.0001 ... Solyc01g000020.1.1 3.64 0.0032 ... ...
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