Pairwise Sequence Alignment

About Pairwise Sequence Alignment

This tool aligns two DNA or protein sequences end to end with the Needleman-Wunsch algorithm. You set match, mismatch and gap scores, and it returns the optimal alignment, its total score, the percent identity and a text view with vertical bars marking matching columns.

How to use it

1. Paste the first sequence into Sequence A and the second into Sequence B.
2. Adjust Match, Mismatch and Gap scores under Scoring, or leave the defaults of 1, -1 and -2.
3. Read the Score, identity percentage and matches badges under Global alignment.
4. Study the wrapped alignment, where A and B are stacked with a bar between identical residues, and copy it with Copy alignment.

The default demo pair

A = GATTACA, B = GCATGCU (match 1, mismatch -1, gap -2)

No gaps. Score -1, 3 of 7 columns match, 42.9% identity. Aligned columns: G=G, T=T, C=C.

When to use it

• Comparing a sequenced clone against its reference to locate differences.
• Measuring how similar two short protein or DNA fragments are.
• Learning dynamic programming by seeing how gap and mismatch penalties change the alignment.
• Checking an amplicon sequence against the expected product.

Questions about Pairwise Sequence Alignment

What does global alignment mean here?

Both sequences are aligned along their full length. If one is a short fragment of the other, its ends are penalized as gaps. A local method would be better for that case, and this tool does not offer one.

How is identity calculated?

Identical columns divided by total alignment length, counting gap columns in the denominator, so extra gaps lower the percentage.

Does it use BLOSUM or PAM matrices?

No. It uses a flat match and mismatch score with a single linear gap penalty, so it cannot rank conservative substitutions above unrelated ones in proteins.

Why no gaps in my alignment?

When a gap costs more than two mismatches, as with the default of -2 against -1, the algorithm prefers mismatches. Make gaps cheaper to see them appear. Note that T and U are different letters.

Related tools

• DNA Reverse ComplementReverse, complement, or reverse-complement a DNA or RNA sequence (IUPAC ambiguity aware).
• DNA to RNA TranscriptionTranscribe a DNA coding or template strand into mRNA, or reverse-transcribe RNA back to DNA.
• DNA to Protein TranslationTranslate a DNA or RNA sequence into protein across reading frames using the standard genetic code.
• ORF FinderFind open reading frames (ATG to stop) across all six frames, with position, length, and protein.
• GC Content CalculatorCalculate GC%, AT%, base counts, and a basic melting temperature for a DNA sequence.
• Sequence StatsLength, base composition, GC%, and approximate molecular weight for raw or FASTA sequences.