Stacking up of matching database sequences is a common characteristics for the alignment displays obtained using -m 1 to -m 6. In -m 1, or query anchored showing identity, the query sequence is kept as it is except for the filter masked region, which is shown as n for nucleotide or x for protein. Matching database sequences are shown underneath the query. If the database sequence is the same as that in the query in a position, the base or residue in that position will be replaced by a dot (.). Alignment gaps in the database sequence are shown as -, while alignment gaps in the query will be shown as insertions in the database sequence(s).
In Figure 6.3.2, the query is identified by 2_0. Since we did not specify -J in the command line, BLAST assigns arbitrary ids to the queries. To show the actual seqID, add -J T to the command line.
This display format is useful in identifying potential pattern of changes among the database sequences aligned to the same region of the query. For example, aligning the mRNA of a gene to est database and displaying the result in this format can help identify potentially novel SNPs for this gene.
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Figure 6.3.2 Alignment (-m 1) display of a standalone blastn
search result.
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Note:
A identities to the query in database sequences are replaced with .
B gaps in the query are shown as insertions in database sequences (after \ marked position)
C the difference is shown as it is in database sequence, and ns are filter masked region of the query
D insertions in the query is shown as gaps in the database sequences