The in-house developed Antigenic Variability Analyser tool (AVANA) was subsequently used to extract alignments of several subsets of the collected sequences, based on annotation values, such as viral subtype, host, and year of isolation.
The genomic coordinates of the predicted sites were then used to extract alignments that covered 400 nucleotides upstream or downstream of the miRNA match in the following species: mouse - mm8 assembly, rhesus monkey - rheMac2 assembly, dog - canFam2 assembly, cow - bosTau2 assembly and horse - equCab1 assembly.
Multipipmaker [25] was used to align the rat GC-D genomic sequence with the resulting scaffold sequences, as well as GC-D genomic sequences identified in the mouse, dog, macaque, chimpanzee and human genome assemblies, and the tool subalign [25] was used to extract alignments of each GC-D exon.
Alignments were filtered using pslcDNAfilter from the BLAT suite to extract alignments with 97 % minimum identity and 30%% minimum query coverage.
It further allows for the implementation of SAMtools to extract alignments in a region, merge and sort alignments and to complete SNP calls [ 20, 21].
Users can use SAMtools (http://samtools.sourceforge.net) to extract alignments in a region, merge/sort alignments, get single nucleotide polymorphism (SNP) and indel calls and visualize the alignment.
A mask is generated to document positions of the all-gapped columns in the extracted alignment and the all-gapped columns are subsequently trimmed to produce an alignment profile.
We extracted alignment fragments overlapping the putative promoter regions and the in -vivo bound regions.
17 From calculated pairwise sequence alignments PROVEAN extracts alignment scores between an unmutated query protein sequence, a query sequence with introduced amino acid variants, and closely related homologous proteins that are known to be functional.
See Algorithm 3. The C_PBNA algorithm can be roughly divided into three steps, constructing the support matrix, calculating the eigenvector of the matrix, and extracting alignment results, as in Figure 2.
