MacVector makes comparing sequences exceptionally easy. Here's a brief overview on the many different tools that you can use to align two or more sequences.
The tool to which most people first turn to for aligning sequences is the Multiple Sequence Alignment tool. This allows you to align multiple DNA or protein sequences using either Muscle, Clustalw or T-Coffee. This functionality is most suited for protein alignments, or for nucleic acid sequences where you are interested in examining phylogenetic relationships.
At some point all molecular biologists have to verify that a sub cloning procedure has worked or a new construct is correct. The Align to Reference tool is perfect for quickly verifying a set of sequencing reads against a reference
Align to Reference can also be used to align cDNA clones against a genome sequence. The steps are similar – use the genomic sequence as the reference, then add one or more cDNA clones to the alignment.
This “Dot Plot” function is great for identifying weak regions of similarity between two sequences. Dot Plots are also the best way of identifying sequence rearrangements
Use this to identify and align a sequence to the databases at the NCBI using the BLAST algorithm. You can download any hits directly to your Desktop including all annotations.
Align to Folder allows you to scan a local folder full of sequences and align them using the FastA alignment algorithm. Its kind of like a local BLAST, but more sensitive.
This requires our optional Assembler add-on. Use this if you want to align ten or more DNA sequences with the idea of assembling them into a longer sequence with a consensus (de novo) or for aligning reads against a reference (resequencing).