Alternate Alignment Views

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The default Pairwise view shown in Figure 1-10 is the classic BLAST output style,

but other options are available for other purposes. These options, described in the

NCBI reference section and in Appendix A, include pairwise, query-anchored with

identities, query-anchored without identities, flat query-anchored with identities, flat

query-anchored without identities, and Hit Table. The most friendly option for text

parsers is the Hit Table, which is viewed in plaintext format. This displays all the

results in a tab-delimited table, which can be parsed easily. You can select this at the

top of the page by changing “Format” to “Plain text” and “Alignment view” to “Hit

Table” (Figure 1-12).

The Hit Table alignment view is shown in Figure 1-13. The first five lines start with

# and are comments about the BLAST program, the query, and the database, fol-

lowed by a description of the reported fields. The lines after the comments are the

alignments in table format. The Hit Table contains all the necessary data to judge a

hit without displaying the actual sequence being aligned.

Figure 1-12. Changing format options

Figure 1-13. Hit Table alignment

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Table of Contents for Alternate Alignment Views