User GuidesSnapGene FAQ Alignment and AssemblyWhat Alignment and Assembly tools are Available in SnapGene?

What Alignment and Assembly tools are Available in SnapGene?

SnapGene has tools for:

  • Aligning sequences to a reference sequence
  • Pairwise/multiple alignment of related sequences
  • De novo assembly of Sanger reads

Alignment of sequences to a reference

The "Align Sanger Reads to a Reference" tool is an 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 you can check and validate your cloning or mutagenesis experiments by aligning Sanger reads 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 article Align Sanger Reads to a Reference 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 reads derived from the same source genome/clone/sequence.

This tool can be used to assemble Sanger reads to generate one or more contigs and 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 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.

See the Guide chapter  Pairwise and Multiple Alignment to learn more about performing multiple alignments in SnapGene.

The SnapGene pairwise alignment tool uses Parasail to align and compare two DNA and/or RNA sequences, or two protein sequences.

The pairwise alignment tool can be used to align and compare two related sequences.

See the Guide chapter  Pairwise and Multiple Alignment to learn more about performing pairwise alignments in SnapGene.