Pairwise Align Codons

Format Conversion

-Combine FASTA
-EMBL to FASTA
-EMBL Feature Extractor
-EMBL Trans Extractor
-Filter DNA
-Filter Protein
-GenBank to FASTA
-GenBank Feature Extractor
-GenBank Trans Extractor
-One to Three
-Range Extractor DNA
-Range Extractor Protein
-Reverse Complement
-Split Codons
-Split FASTA
-Three to One
-Window Extractor DNA
-Window Extractor Protein

Sequence Analysis

-Codon Plot
-Codon Usage
-CpG Islands
-DNA Molecular Weight
-DNA Pattern Find
-DNA Stats
-Fuzzy Search DNA
-Fuzzy Search Protein
-Ident and Sim
-Multi Rev Trans
-Mutate for Digest
-ORF Finder
-Pairwise Align Codons
-Pairwise Align DNA
-Pairwise Align Protein
-PCR Primer Stats
-PCR Products
-Protein GRAVY
-Protein Isoelectric Point
-Protein Molecular Weight
-Protein Pattern Find
-Protein Stats
-Restriction Digest
-Restriction Summary
-Reverse Translate
-Translate

Sequence Figures

-Color Align Conservation
-Color Align Properties
-Group DNA
-Group Protein
-Primer Map
-Restriction Map
-Translation Map

Random Sequences

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-Random Coding DNA
-Random DNA Sequence
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Sequence Manipulation Suite:

Pairwise Align Codons

New version available: Sequence Manipulation Suite 3 (SMS3)

Pairwise Align Codons accepts two coding DNA sequences and determines the optimal global pairwise alignment at the codon level using an affine gap penalty model. Alignment is scored using the empirical codon substitution matrix of Schneider et al. (2005) (BMC Bioinformatics 6:134), which assigns log-odds scores to all 64×64 codon pairs based on observed substitution frequencies across aligned protein families. Gaps are represented as triplets (---) to preserve codon structure. Only the bases A, C, G, T, and U are accepted; U is treated as T. Input sequences must be divisible by 3.

Paste sequence one (in raw sequence or FASTA format) into the text area below. Input limit is 20,000 characters.

Paste sequence two (in raw sequence or FASTA format) into the text area below. Input limit is 20,000 characters.

Use the following parameters to specify how alignments are scored.

Gap opening penalty
Gap extension penalty

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