Thus, comparative positions of anonymous markers without direct human alignments were established by performing sequence similarity search on the human genome sequence with bovine WGS contig sequences containing the targeted marker sequences.
All sequence chromatograms were controlled manually and sequence alignments established in BioEdit [ 41] by manual adjustments.
The medication decision, which will bring the track into alignment with standards established by the International Federation of Horseracing Authorities, is believed to be without precedent in North American racing.
The genomic structure of each gene was established by alignment with its cDNA sequence.
Other contigs were established by alignment to the reference (M. musculus) sequence (see below).
The intron-exon structure of the barley MIRNA genes was established by alignment of the pri-miRNA sequences coming from RACE and RT-PCR experiments with genomic fragments obtained by genome walking, as well as by using the FSPLICE program [ 53].
Since lack of sequence conservation prevents establishing orthology by alignment, we limited our search to intronic sequences whose orthology was established by aligning their bracketing exons.
In the 1D 1D mapping established by sequence alignments it is not possible to have many-one relationships, for example, however once the distance cutoff exceeds a certain level it is possible for the optimal set of equivalences to contain many-one pairings since several regions might be equally related via duplication.
The domain composition and order found in ORF2 was established by performing multiple alignments of the putatively active Ty1/copia-like elements from P. tricornutum and T. pseudonana with Ty1 from yeast and Copia from fruit fly and of the putatively active Ty3/gypsy-like elements from T. pseudonana with Gypsy from fruit fly, and Ty3 from yeast.
A significant similarity of this region was established by running HHPRED against a collection of alignments assembled from Pfam and other domain alignments (KH, unpublished) (Soding et al, 2005; Punta et al, 2012).
Pairwise alignments were generated and compared among ITS sequences for similarity, which was established by dividing the number of matching nucleotides by the total length of the alignment using the online version of Needle in EMBOSS [42] [42].
