AGA - Annotated Genome Aligner

AGA needs a reference genome (GenBank record) and a query sequence (FASTA format).
Click here to load some sample data.

Reference genome

Query sequence

The following set of parameters affect the nucleic acid sequence alignment score

Weight

Weight of nucleotide alignment score in total score

Gap open penalty

Penalty for opening a gap (affine gap model)

Gap extension penalty

Penalty for extending a gap (affine gap model)

Match score

Score for a matching nucleotide in reference and query

Mismatch score

Score for a different nucleotide in reference and query

The following set of parameters affect the amino acid sequence alignment scores for each CDS

Weight

Weight of amino acid sequence alignment score in total score

Gap open penalty

Penalty for opening a gap in a CDS (affine gap model)

Gap extension penalty

Penalty for extending a gap in a CDS (affine gap model)

Substitution weight matrix

Substitution weight matrix for scoring matching amino acids

Frameshift penalty

Penalty for an (unlikely) gap that causes a frameshirt in the query or reference sequence

Codon misalignment penalty

Penalty for a gap that is not codon-aligned (causing 'X'-es in the amino acid sequence)

Choose what kind of alignment you would like:

Global alignment (using the complete query sequence)

Local alignment (using only matching part(s) of the query sequence)

Tip: use global alignment only if you really demand that the entire sequence matches