Script Specifications

Some calculations are made to transform the row data outcomming from the program in something more understandable. First of all a counter for each region (exon, intron, acceptor or 'pre' and donor or 'post') is initialized. This will be useful while counting the total exon occurrences in a gene, for example. An other counter is set for measuring the region wideness (that is limited by the initial 'ini' and final 'end' coordenate when the region is entering in the checkcoords subroutine). Then SNPs density can be calculated as the total number of occurences in a region divided by the total number of basepairs in that region.

In addition we included in our study the calculation of the distance between consecutive SNPs in a given region. This distance is only calculated when two consecutive SNPs are found in the same genomic region. That means that, if a gene has two SNPs in exons, but they are placed in different exons, the distance would not be calculated.

Finally, this data has to be prepared in order to be uploaded to the web. While this transformation happens, some additional calculations are performed. All individual data (for each gene) is compared with the global data (the ponderated mean of all chromosomes results) , so the relative abundance of SNPs in region can be obtained referring to the global data. In the summary page, for each chromosome, we display those genes that have 5 times more SNPs/Kb in exon regions that the mean value (SNPs High Density Genes) and those genes that have 5 times less SNPs/Kb in exon regions that the mean value (SNPs Low Density Genes). In the summary page, 'Hot points', those SNPs placed in splicing sites, are also avalaible for each chromosome.