Exercises for the Basics tutorial

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Pairwise alignment

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Pairwise alignment: dot plot

Searching for annotations based on their sequence

We will use an annotated vector sequence to annotate unannotated vector sequences. The Workbench comes with a list of vector sequences, some of them annotated some of them not. In the "Example Data" folder, expand the "Cloning vector library". As you can see it contains many vector sequences but when you open and cicularize the first vector: "M13mp8_pUC8" or vector "pAT153" you can see that they do not contain any annotations.
When you open and circularize "PCS19" on the other hand, you see that it is well annotated.

Please note that the Workbench comes with a list of motifs for annotations. You can find them in the "Example Motifs" file in the "Enzyme lists" folder in "Cloning" section of the "Example Data". When you open this file you see that it contains among others motifs for the start codon, the hexaHis tag, primers for various promoters...

The Workbench contains by default a list of vector sequences but this list is not complete and some vectors are not annotated. Since adding and annotating vector sequences to the Workbench is a cumbersome task, you can download an extensive list of annotated vector sequences, compiled by BITS. You can simply import this list into a folder in your Workbench.