An evolutionary trace analysis of TK domain and VFTM of VKR was performed after aligning sequences of each domain, including those from insects and other invertebrates (S. mansoni and S. purpuratus).
By aligning sequences of intergenic regions of Borrelia species available in the GeneBank we were able to identify regions of homology that were used to design primers (Table 2) for amplification and sequencing of four overlapping fragments covering the entire region between the Ile tRNA and the 23S rRNA genes (Table 2).
This was demonstrated by aligning sequences of various lengths by the positions of their longest identical segments.
In this paper, the authors study the parallel (and divergent) replacement of residues of proteins in different evolutionary paths, obtained by aligning sequences of three quartets of organism.
Conservation was analyzed by aligning sequences of 21 species in total (21 α, eight β and six γ sequences, comprehensive list in Additional file 1: Supplementary materials).
To design primers for nine-spined sticklebacks, conserved regions were searched in microsatellite flanking regions by aligning sequences of the three-spined stickleback and medaka [ 37].
For fragments 6.8 k and 7.6 k, which overlap with repetitive sequences, search for possible cross-amplification was performed by aligning sequences of these amplicons to available wheat shotgun sequences, using BLASTN searches (http://wheat-urgi.versailles.inra.fr/Seq-Repository/BLAST) on the IWGSC wheat shotgun sequences (http://www.wheatgenome.org/).org/
In the case of Zip, there is considerable length of aligning sequence after the last TM block that is part of Pfam's Zip domain.
By aligning sequence reads of each individual DH line to the PRF, both allelic SNP and presence/absence variations (PAVs) were discovered and genotyped.
For analyzing ribosomal RNA genes, putative secondary structures of 22 tRNA genes were identified using tRNAscan-SE [ 34], or by recognizing potential secondary structures and anticodon sequences by eye by aligning sequences with those of A. simplex and A. suum.
The target genome sequences (chicken, turkey, or zebra finch) when not placed on specific chromosomes were discounted when calculating amounts of aligning sequence; such amounts are thus likely to be conservative estimates.
