SnapGene has alignment tools for:
- Aligning DNA sequences to a reference sequence
- Multiple alignment of related DNA, RNA and protein sequences
- Pairwise alignment of related DNA, RNA and protein sequences
- De novo assembly of Sanger reads
Alignment of sequences to a reference
The "Align to Reference DNA Sequence" tool is a DNA alignment tool. It is not an "Map to reference" assembly tool. All sequences/reads are aligned independently to the reference sequence.
You can use the "Align to Reference DNA Sequence" tool to check and validate your cloning or mutagenesis experiments by aligning Sanger reads or whole plasmid sequencing results to a reference sequence.
You can also use this tool to "map" mRNA or cDNA sequences to a genomic sequence - see Create a Feature with Introns Using an Aligned cDNA.
See the Guide articles Align Sanger Reads to a Reference Sequence and Align a "Whole Plasmid Sequence" to a Reference Plasmid Sequence to learn more about aligning sequences to a reference.
Assemble Contigs
The "Assemble Contigs" tool is a de novo Sanger sequence assembler, based on the CAP3 algorithm.
This tool should only be used to assemble DNA sequence reads derived from the same source genome/clone/sequence.
This tool can be used to assemble Sanger reads to generate one or more contigs to create consensus sequences.
See the Guide article De Novo Assembly of Sanger Sequences to learn more about assembling Sanger reads.
Multiple Alignment of Related Sequences
SnapGene provides four third-party multiple alignment tools that you can use to align three or more DNA and/or RNA sequences, or three or more protein sequences:
- Clustal Omega
- MAFFT
- MUSCLE
- T-Coffee
These multiple alignment tool can be used to align and compare related sequences.
These multiple alignment algorithms do not test or correct fragment orientation, so ensure all input sequences are in the same orientation. Use Flip (reverse complement) a dsDNA sequence first if required.
See the Guide chapter Pairwise and Multiple Alignment to learn more about performing multiple alignments in SnapGene.
Pairwise Alignment of Related Sequences
The SnapGene pairwise alignment tool uses Parasail to align and compare two DNA and/or RNA sequences, or two protein sequences.
The pairwise alignment algorithm options are:
- Local alignment (Smith-Waterman)
- Global (Needleman-Wunsch)
- Semi-Global
The pairwise alignment tool can be used to align and compare two related sequences.
See the Guide chapter Create a Pairwise Protein Alignment to learn more about performing pairwise alignments in SnapGene.