The sequence reads for GFP and Input were aligned to the reference mouse genome (mm9, build 37) using Bowtie 2 software (version 2.2.2) [ 45].
The sequence tags for RNAPII Ser2P and Ser5P and Input were aligned to the human genome (hg19) using Bowtie [ 31] software.
For example, input data organization 1 is when input data is aligned along Nc dimension as a level 1, Np dimension in level 2, and Nr dimension in level 3. Input data organization 2 is as like input data organization 1: input data is aligned along Nc dimension as a level 1, but Nr dimension is in level 2 and Np dimension in level 3 (Figure 16).
After submission through this interface, each input protein is aligned using an HHsearch-based protocol against the Virfam collection of 28000 profiles generated for the present work.
If a single input contig is aligned to several Velvet contigs, we connect these Velvet contigs to a walk in the assembly graph.
Data preprocessing: in our study, we assume that the input data is aligned correctly and focus specifically on the problem of identifying somatic mutations from allelic counts extracted from perfectly aligned data.
Therefore, in order to overlap the input data well, the reference data is aligned by means of a particle filter.
"Finally everything is aligned".
Let F = { f i|i = 1,..., N} be the set of input fragments which are supposed to be aligned to the reference genome, and each fragment f i takes value f ij ∈ Σ at locus j ∈ X if a nucleotide is aligned and equal to one of two alleles, and f ij = ∅ if fragment f i is unaligned, gapped, ambiguous, or a base different from the two alleles, at site j.
All unique sequences from the input samples are aligned to the genome of interest using the Eland alignment tool (step 5).
