Figure 2.
Example of NAST compression of a BLAST pairwise alignment using a 38 character aligned template. Template and candidate is extended to 40 characters after (A) BLAST gap insertion and (B) retention of original template spacing. (C) Nucleotide insertions in the candidate relative to the template which force additional characters to be added in the template are identified at positions α and β. (D) A bi-directional search for the nearest alignment space (hyphen) relative to the insertion terminates at the positions indicated by the black arrows. The leftward search from the α position was shorter in distance compared with the rightward, thus the space to the left of ‘GT’ was removed. (E) The search from the β position encountered the alignment edge on the right, thus the position to the left of ‘AC’ was removed. (F) Lastly, the two template-extending spaces are deleted from the template. Notice that sequence data are not added to or overwritten in the candidate. The NAST removal of two characters from both sequences allowed local misalignments (underlined) while preserving the 38 character format of the global MSA.