In the second stage, the partial sequences were aligned to the full-length sequence profile using the guide tree generated during the first stage.
That is, Build a guide tree consisting of N + 1 tips, using the distances calculated in steps 1 and 2. Compute a multiple alignment consisting of N + 1 sequences using the guide tree computed at the previous step.
After determining an optimal consensus level of 50% for the guide sequence used to identify indel boundaries [ 39], we found 4,707 indels in these proteins, of which 901 are classified as simple (binary-state) and 3,806 as complex (multi-state).
The guide sequences in the sgRNAs used for targeting the various loci are shown in Supplementary file 1D.
In theory there are two different ways of using the reference sequence to guide the assembly process.
An NI3C C-cap mutant carrying five additional mutations in the interface to the preceding repeat, previously designed by using the consensus sequence as a guide, showed a rigid-body movement of the C-cap towards the internal repeat.
Rather than sampling sequences, the theory directly provides the site-specific amino acid probabilities, which are then used to guide sequence design.
A method for inhibiting the expression of particular genes using external guide sequences (EGSs) has been developed in bacteria, mammalian cells and maize cells.
Using the protein sequence alignment as a guide, the corresponding nucleotide sequences are subsequently aligned, codon by codon, using pal2nal (Suyama et al. 2006).
Pol sequences were aligned by Muscle in batches of 1000 sequences, then these partial alignments were merged using the HXB2 reference sequence as a guide.
