BlastAlign uses NCBI Blast to align nucleotide sequences that have large indels (INsertions/DELetions) or are otherwise difficult to align globally. The program selects the most representative sequence from the input sequences and then extracts the blast query anchored multiple alignment (in NEXUS and Phylip formats). Alternatively, the user can choose which sequence to use as an anchor. The program also outputs a matrix representing regions of homology along the sequences, which can be used to visually identify subgroups sharing particular large indels. An additional program, BlastAlignP uses tblastn to align nucleotide sequences to a single amino acid reference sequence, allowing an open reading frame to be maintained in the multiple alignment.
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Belshaw R, Katzourakis A. 2005.
BlastAlign: a program that uses blast to align problematic nucleotide sequences.