Sequence Alignment

Determining how similar or different two sequences are to each other is a common approach for inferring structural, functional or evolutionary relationships between two sequences. VectorBuilder’s Sequence Alignment tool allows you to not only directly compare two sequences at the DNA or protein level, but also compare two DNA sequences based on translation.

Alignment provides a global perspective with percent identity/similarity across entire sequences and a focused perspective comparing individual nucleotides/amino acids. This tool utilizes gaps and gap penalties to maximize the chances of matching two nucleotides or amino acids while maintaining data integrity. While gaps account for insertions or deletions in the aligned sequences, gap penalties assign negative scores to the alignment based on the frequency and length of the gaps.


  • Sequences in both GenBank and FASTA formats can be recognized.
  • Max sequence length 10,000 bases or 10,000 amino acids.
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