GeneQuest Methods - User Guide to GeneQuest - 17.3

The following table lists methods you can drag onto the Assay Document, including many methods designed to find potential genes.

Task	Apply this method
Display the sequence on the document	Apply Sequence.
List known features for the sequence.	See Annotate Features.
Add a document title	Apply Title.
Add a ruler	Apply Ruler.
Plot the local frequency of particular bases	To plot the local frequency of the four bases and A+T and G+C pairings and the local strand skew of the complements AT and GC, apply Base Contents – Base Distribution.
Predict the bending of free DNA	To predict the bending of free DNA by showing localized angles of helix trajectory computed for a specified window size, apply Bent DNA – Bending Index.
Find genes using coding region recognition algorithms	Three methods use coding prediction algorithms to find potential genes. To use Borodovsky’s Markov method to identify potential coding regions, apply Coding Prediction – Borodovsky. To use the Shannon information theory to find regions rich with information, apply Coding Prediction – Local Compositional Complexity. Use open reading frames (ORFs), apply Coding Prediction – Starts Stops ORFs. This method locates and summarizes open reading frames longer than a user-specified minimum length. You can designate whether or not a start codon is required. Starts and stops are displayed independently for all frames.
Apply restriction enzymes to the sequence	To create restriction maps using any of the enzymes from the DNASTAR enzymes catalog, apply Enzymes – Restriction Map.
Find matches to a user-specified sequence file	To identify regions that match those of a user-specified DNA sequence file, use Gene Finding – DNA Finder. This method displays results separately for the top and bottom strands. To identify regions whose translation matches a user-specified protein sequence file, use Gene Finding – Protein Finder. This method’s display combines results for all six reading frames.
Find genes using patterns	Three methods use patterns to locate potential genes: To use log odds or positional frequency matrix patterns to locate starts, stops, and intron & exon splice sites, apply Patterns – Matrix. To use a text-based pattern database of known DNA transcription factor sites, apply Patterns – Signal. To use patterns you type in, apply Patterns – Type-In Pattern.
Find genes using repeats	Three methods use repeat locations to locate potential genes: To locate dyad repeats and palindromes, apply Repeats – Dyad Repeats. To locate direct repeats, apply Repeats – Direct Repeats. To locate inverted repeats, apply Repeats – Inverted Repeats.

Base Contents – Base Distribution

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