GeneCoder: Restriction Enzyme Sequence Analysis

Articles —> GeneCoder: Restriction Enzyme Sequence Analysis

Restriction Enzyme cut DNA sequences at specific sequences, or sites. There are hundreds of known enzymes, many with distinct target sequences. GeneCoder is supplied with over 100 such sequences and anayzes DNA sequences for such sites on the fly.

Viewing Sites

Each sequence view shows Restriction Sites in different ways. The sequence editor gives an overview of all chosen enzymes, those which don't cut are dimmed to the color gray. This table can be sorted by clicking the table header, and to see where each enzyme cuts, right click the enzyme which will show its cut positions. One can also quickly remove an enzyme from the chosen enzymes by double clicking the enzyme in the table, or right clicking the enzyme and choosing preferences.

GeneCoder Restriction Enzyme Table

Restriction enzyme table showing all restriction sites which cut a particular sequence. Right clicking an enzyme allows further options.

Changing Enzymes

Given the large number of enzymes in GeneCoder, using them all can result in clutter and confusion. To change which enzymes are used in analysis, go to Reference -> Enzyme Preferences. The pop-up dialog shows all restriction enzyme data and allows you to alter which enzymes will be used in analysis.

GeneCoder Restriction Enzyme Preferences

Restriction enzyme preference window.

Enzyme Digests

The Digest view panel facilitates analysis of a sequence when digested with restriction enzymes. Double click an enzyme to add it to the digest. To remove the enzyme, click the '-' button in the lower right enzymes panel. The view shows lengths of fragments expected from the digest. To use or share this as an image, right click the panel and choose the appropriate action.

GeneCoder Restriction Enzyme Digest

Restriction enzyme preference window.

1Given that longer sequences will slow down GeneCoder, restriction sites are only determined for sequences < 10000 nucleotides in length. This parameter can be changed by going to Preferences -> Enzymes and entering in a new value.

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