Sequence alignment and sequence assembly are very different workflows, but the terms are often used incorrectly. Adding to the confusion, both workflows can involve an optional “reference” sequence, and both can use some of the same sequence file types. This topic defines each workflow and recommends the best Lasergene application to use in different scenarios.
Are your sequences from different organisms or strains?
If so, you will want to perform sequence alignment with MegAlign Pro.
Sequence alignment is used to investigate the evolutionary relatedness of two or more organisms or strains, and the creation of a phylogenetic tree is often the end goal. MegAlign Pro lets you align DNA, RNA or protein sequences from a single gene up to an entire genome. The sequence files used in this workflow typically have formats like .fasta, .seq, .pro, .genbank.
Using a reference sequence in multiple sequence alignment is optional, but can be used to guide a MAFFT alignment.
Do your sequences consist of sequencing reads from one individual DNA sample?
If so, you will want to perform sequence assembly using SeqMan Ultra for Sanger trace data reads (e.g., .abi) and SeqMan NGen for all other read types (e.g., .fasta, .fas, .fastq). In this workflow, longer consensus sequences (“contigs”) are assembled from short fragments of a single DNA sample.
Both SeqMan Ultra and SeqMan NGen allow you to assemble the reads de novo or by using a “reference” sequence as a template. Using a reference in sequence assembly allows the software to assemble DNA fragments into larger contigs faster and more accurately than assembling them de novo.
As with MegAlign Pro, the use of a reference sequence in sequence assembly also allows you to explore variants between the sequence reads/contigs and the reference sequence. Variants resulting from sequence assemblies in Lasergene are viewed using graphical views and tables in SeqMan Ultra and ArrayStar.
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