The equalizer filters, as well as the ordering by which the streams are extracted, are updated based on the minimization of a set of least squares (LS) cost functions in a BLAST-like fashion.
The regions of the scaffolds corresponding to significant matches, plus an additional 2000 bases up- and down-stream, were extracted as a single unit using a Perl script.
The palindromic score function works as follows: for every instance of a small RNA aligning to the genome, the alignment plus 50 bases up and down stream were extracted.
The process is repeated until the whole binary data stream is extracted.
The road and streams data were extracted from 1 50,000 topographic maps of the study area, which were used to create digital elevation models (DEMs) that were in turn used to derive the slope and aspect data.
Areas of the sub-watersheds along with their perimeter, elevation information, basin length, and number and length of stream networks were extracted for further analysis.
The stream orders were extracted from Cartosat-I DEM (10 m) and updated from SOI toposheet of 1 50,000 following a system introduced by Horton (1945) but later modified by Strahler (1952).
RGH DNA sequences including additional 2,000 bp up- and down-stream sequences were extracted from the Gy14 draft genome scaffolds and re-annotated with Augustus (http://bioinf.uni-greifswald.de/augustus/) using 9930 CDS (Version 2.0) [ 26] as reference sequences.
IS 6110 elements were identified in each genome using blast with an e-value threshold < 1e-30; 200 bp of the up-stream and down-stream flanking sequences were extracted for each insertion identified.
Watershed boundary and stream network data were extracted from the National Hydro Network (NHN) data on the GeoBase Web portal of Canada.
