Similar to (3), a basic threshold value is calculated by processing the sequence in (4) with the aforementioned filter (1 − z−16384 /(1 − z−1), and a decisive threshold value is also defined as two times of the basic threshold.
Using SitePainter, we were able to rapidly deduce which bacteria were in different regions of the hand, along with a graphical representation of microbial abundances by processing the sequence data with QIIME (Caporaso et al., 2010) and mapping the abundance of each taxon onto the hand image (Fig. 1B).
An optimal peak chart was obtained by processing the raw sequence data with basecalling.
Note that we have thus computed 50/ F P distribution features by processing the protein sequence starting from the first row of the PSSM in downward direction.
As in section 1, loading and processing the sequence is handled automatically by the instantiation of the USM object.
Chimeric sequences were screened by processing the BLAST results [ 12] using Arabidopsis thaliana ftp://ftp.arabidopsis.org/home/tair/Sequences/ as reference dataset and a SGN Perl script.
To exclude sequences including errors caused by biochemical and/or by sequencing processing, the sequences were additionally checked for the presence of the flanking nucleotides.
Our final database of non-redundant filter sequences was prepared by processing all filter sequences through the NCBI BLASTclust program [ 69] with the identity and coverage parameters set to 90% (i.e., pairwise matches require sequences to be 90% identical over 90% of their lengths).
Expressed candidate Helitrons were identified by batch processing the putative Helitron sequences through the National Center of Biotechnology Information, NCBI (www.ncbi.nlm.nih.gov) BLAST (Basic Local Alignment Search Tool) analysis against the Expressed Sequence Tag (EST) database of Z. mays.
Each primer pair was designed by processing available sequences using CLC Combined Workbench 3 Software (CLC-Bio, Denmark), and the properties of each primer were verified using Primer Tool (Sigma-Aldrich, USA; http://www.sigmagenosys.com/calc/DNACalc.asp).sigmagenosys.com/calc/DNACalc.asp
