calculate_G4_density.pl

This Perl program takes a tab separated file holding G4 starting and ending locations as input and calculates the number of G4 on both DNA strands at specific bin sizes along chromosomes. Additional information regarding the use of the program can be found at the top of the file. <br

calculate_HBS_density.pl

This Perl program takes a tab separated file holding histone binding site starting and ending locations as input and calculates the number of sites at specific bin sizes along chromosomes. Additional information regarding the use of the program can be found at the top of the file

calculate_GeneTranscript_density.pl

This Perl program takes a tab separated file holding gene transcript starting and ending locations as input and calculates the number of transcripts on both DNA strands at specific bin sizes along chromosomes. Additional information regarding the use of the program can be found at the top of the file

Typical Radial Basis Function network topology.

<p>Typical Radial Basis Function network topology.</p

Sub-regions and oligonucleotide lengths considered for feature extraction.

<p>Sub-regions and oligonucleotide lengths considered for feature extraction.</p

Training sequences are divided around the TSS with overlapping regions.

<p>This specific subdivision shows feature 7 settings, as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004878#pone-0004878-t001" target="_blank">Table 1</a>.</p

ROC curve for chunk sizes 50 and 500.

<p>Both axes are scaled to logarithm base 10 to highlight the difference.</p

PRC curve for chunk sizes of 50 and 500.

<p>PRC curve for chunk sizes of 50 and 500.</p

Area under the curve for RBF-TSS and ARTS.

<p>Area under the curve for RBF-TSS and ARTS.</p

The number of putative G4 sequences and the percentage identified with different numbers of guanine tracts.

<p>The number of putative G4 sequences and the percentage identified with different numbers of guanine tracts.</p