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A fitting sequence alignment aligns all of a short query to a substring of a longer target, leaving target flanks unpenalized. It differs from unrestricted local sequence alignment, which may also omit part of the query.

Use local sequence alignment, such as the Smith-Waterman algorithm, to compare the globin fragment with the matching region of each full-length target. A global sequence alignment would penalize long target flanks absent from the fragment. For a linear gap penalty the dynamic programming recurrence includes a restart option:Initialize boundary entries to zero, start traceback at the largest entry anywhere, and stop at zero. If the entire query is known to be valid and must be retained, fitting sequence alignment is a suitable refinement: align the whole fragment while leaving target flanks unpenalized.

First check the sequence alphabet: the prompt calls the targets “genes”. If the FASTA format file contains DNA rather than protein, translate the relevant coding sequences into amino acids before a protein-to-protein sequence alignment. If coding frames are unknown, search translated frames. A file in FASTA format specifies storage syntax, not whether the contents are nucleotides or residues.