Because MacVector includes custom feature appearance information when annotating the sequence, you can use this to maintain a carefully curated set of your favorite genes and sequences each with a graphical appearance that best suits your needs.Update 19 August 2013: We’ve added support for Muscle and T-Coffee to the MSA editor You can scan an unannotated or partially annotated sequence against a folder on your hard drive and MacVector will identify matching features in sequences in the target folder and add them to your sequence. We get a lot of comments and questions from users on the various alignment functions in MacVector. They say there’s more than one way to skin a cat (not that I’ve done that – I have skinned a catfish, but I only know one way), and thats certainly true for alignments in MacVector. ClustalW – we also call this the “standard” Multiple Sequence Alignment (MSA).Įach function is designed for a different purpose.Pustell Matrix (also known as a Dot Plot)ĬlustalW/Multiple Sequence Alignment (MSA).If you have two or more related sequences (DNA or Protein) and you want to examine the relationship between them, use this function. Choose File->New->Protein Alignment (or File->New->Nucleic Acid Alignment) to create an empty MSA window. Add sequences to the alignment by using the Edit->Add Sequences from File menu item then click on the Align toolbar button to automatically align the sequences using ClustalW. Click on the Prefs toolbar button to control the appearance and behavior of the data in each of tabs that represent different views or analyses of the alignment. This functionality is most suited for protein alignments, or for nucleic acid sequences where you are interested in examining phylogenetic relationships. If you wish to compare two or more DNA sequences, you should definitely consider if one of the other alignment functions may be more suitable. Use this if you have a reference sequence and you want to align one or more DNA sequences against it. A typical use would be in resequencing e.g. sequencing a cloned PCR fragment to check no errors were introduced, sequencing across end junctions, scanning for successful mutagenesis clones etc. In each case, open the file that represents the parent or “reference” sequence, then choose Analyze->Align to Reference. In the window that opens, click on the “+” button to add sequences from disk – these can be in any format that MacVector can read – typically ABI or SCF chromatogram files, but you can add plain sequences as well. When you click on the Align button, choose the Sequence Confirmation algorithm – this is tuned to expect the small insertions/deletions you would expect in raw chromatogram files. Compared to ClustalW, Align to Reference has the advantage that it will automatically “flip” sequences to guarantee optimal alignment.Īlign 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. Repetitive sequence elements identified using a dot plot Now choose the cDNA Alignment algorithm when you Align – this is tuned to expect large insertions representing the intron regions. This “Dot Plot” function is great for identifying weak regions of similarity between two sequences.
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