Creating Custom Interfaces

By The SEED Team on June 3, 2010 2:37 PM
Suppose that you had substantial expertise in graphical interfaces, understood the power of comparative analysis, and wished to support the ability to graphically display the chromosomal regions around a set of genes (normally from distinct genomes). The SEED offers one alternative for doing this (see the region displayed here for an example), but suppose that you did not like forcing users to find appropriate SEED IDs and you thought that you could develop a superior display.

Example 3 illustrates the functions required to determine the location of a SEED gene encoding a specific protein and to acquire the genes from a given region centered on that location. If you were to create a program to accept arbitrary protein IDs, use the conversion capabilities demonstrated in example1, and display the regions graphically around these genes, you would have the core of a useful tool. If you shaded genes from the same subsystem (determined using the capabilities described in example2), you could enhance the supported functionality. Of course, you could also compute which genes could be connected to literature or structures and encode that data as well.

Example Discussion

With the server packages installed, the code in example 3 can be run as follows
> perl server_paper_example3.pl "fig|100226.1.peg.3361" 2000
First, we get the location for the subject ID using the Sapling Server
	my $sapObject = SAPserver->new();
	my $geneLocH  = $sapObject->fid_locations(-ids => [$geneID]);
	my $geneLoc   = $geneLocH->{$geneID}->[0];
Next, we normalize the direction and compute the desired region.
	if ($geneLoc =~ /^(\S+)_(\d+)([+-])(\d+)/)  # retrieve an encoded location
	{
	    my($contig,$beg,$strand,$length) = ($1,$2,$3,$4);
	    my ($left,$right);
         if ($strand eq "+")
         {
             ($left,$right) = ($beg, $beg + ($length-1));
         }
         else
         {
             ($left,$right) = ($beg - ($length-1), $beg);
	    }
	    my $paddedLeft      = ($left > $max_distance) ? $left  - $max_distance : 1;
	    my $paddedRight     = $right + $max_distance;
	    my $sz              = ($paddedRight + 1) - $paddedLeft;
	    my $region          = $contig . "_" . $paddedLeft . "+" . $sz;
Then we use the Sapling Server to retrieve all genes in the region and display the results.
	    my $genesInRegionH  = $sapObject->genes_in_region(-locations => [$region],
	                                                      -includeLocation => 1);
	    my $genesInRegion   = $genesInRegionH->{$region};
	    foreach my $geneID2 (keys(%$genesInRegion)) {
	        my $location = $genesInRegion->{$geneID2};
	        $location =~ /^(\S+)_(\d+)([+-])(\d+)/;
		print "$geneID2\t$1\t$2\t$3\t$4\n";
	    }

 Example 3 Output Table

fig|100226.1.peg.3358	100226.1:NC_003888	3764143	+	867
fig|100226.1.peg.3359	100226.1:NC_003888	3765006	+	504
fig|100226.1.peg.3360	100226.1:NC_003888	3765814	+	360
fig|100226.1.peg.3361	100226.1:NC_003888	3766170	+	612
fig|100226.1.peg.3362	100226.1:NC_003888	3766852	+	489
fig|100226.1.peg.3363	100226.1:NC_003888	3767961	-	606
fig|100226.1.peg.3364	100226.1:NC_003888	3770099	-	2007

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