Pairwise Align Protein

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

-Mutate DNA
-Mutate Protein
-Random Coding DNA
-Random DNA Sequence
-Random DNA Regions
-Random Protein Sequence
-Random Protein Regions
-Sample DNA
-Sample Protein
-Shuffle DNA
-Shuffle Protein

Miscellaneous

-Home
-IUPAC codes
-Genetic codes
-Browser compatibility
-Mirror this site
-Use this site off-line
-About this site
-Acknowledgments
-Reference

home

Sequence Manipulation Suite:

Pairwise Align Protein

New version available: Sequence Manipulation Suite 3 (SMS3)

Pairwise Align Protein accepts two protein sequences and determines the optimal global alignment with affine gap penalties. Use Pairwise Align Protein to look for conserved sequence regions.

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.

Scoring matrix
Gap opening penalty
Gap extension penalty

*This page requires JavaScript. See browser compatibility.
*You can mirror this page or use it off-line.

new window | home | citation Mon Jun 15 14:58:15 2026

Valid XHTML 1.0; Valid CSS