BlastAlign

BlastAlign constructs NCBI blastn-based, query-anchored multiple sequence alignments of nucleotide sequences to preserve regions of homology across sequences with large indels or other structural complexities.

Key Features:

• Alignment Strategy: Builds a matrix representing regions of homology across input nucleotide sequences and selects a 'most representative' sequence to generate a blastn query-anchored multiple alignment, with optional alternative anchor selection.
• Matrix Visualization: Prints the generated homology matrix for visual inspection and identification of subgroups or regions of interest within the aligned sequences.
• Programming Language Integration: Incorporates Perl and Python components and runs on UNIX-based systems (including Mac OSX) and DOS.
• Extended Functionality (BlastAlignP): Uses tblastn to align nucleotide sequences against a single amino acid sequence to maintain an open reading frame in the resulting multiple alignment.

Scientific Applications:

• Comparative Genomics: Aligns divergent nucleotide sequences with large indels to enable sequence comparison across genomes.
• Evolutionary Biology: Preserves homologous regions in alignments for analyses of sequence divergence and evolutionary relationships.
• Functional Annotation of Complex Genes: Supports annotation of genes with complex exon–intron structures by maintaining homology across structurally variable regions.
• Phylogenetic Analysis: Produces alignments that retain conserved regions suitable for downstream phylogenetic inference.
• Identification of Conserved Elements: Facilitates detection of conserved sequence elements across diverse species despite structural variability.

Methodology:

Uses NCBI's blastn to construct query-anchored multiple alignments, builds and prints a homology matrix representing regions of homology, selects a 'most representative' sequence (with optional user-selected anchor) to extract the alignment, and employs BlastAlignP with tblastn to align nucleotide sequences to a single amino acid sequence to maintain open reading frames; implemented with Perl and Python for UNIX/Mac OSX and DOS environments.