Patterns – Matrix

This method, located in the More Methods section, finds sequence features such as start sites, splice acceptor sites and splice donor sites. The matrix patterns are defined in separate data files, which are normally installed in the Matrix Patterns folder, found in the following location:

• Windows: C:\Users\Public\Public Documents\DNASTAR\Lasergene ‘x’ Data

• Macintosh: Hard Drive:Applications:DNASTAR:Lasergene ‘x’

Whereas the start codons identified by the codon prediction method are simply in-frame ATGs, the matrix pattern method takes into account local sequence context with the aim of predicting the subset of ATGs that function as start codons.

The naming convention for matrix pattern files makes it easy to choose an appropriate file. The first few characters of the file name denote the organism; the middle characters describe whether the pattern searches for acceptor splices (as), donor splices (ds) or start sites (atg); and the last digit tells whether the pattern looks for frequencies of nucleotides (1) or dinucleotides (2). Dinucleotide pattern files are less likely to generate false positive results. However, if you fail to locate the patterns you seek using a dinucleotide pattern file, you may observe candidates by using the corresponding mononucleotide pattern file. Also, while the pattern files tend to be species-specific, if there is no pattern file for your organism, you may be able to obtain reasonable results using a pattern file from a similar species.

Note: For a list of species names that correspond to the matrix pattern files, see the file Species Names.txt also located in the Matrix Patterns folder. (See above for the directory path.)

For additional information on using this method, along with a video demonstration, see Look for exons.

To apply the method:

1. Double-click on the method name in the Method Curtain to open the Matrix Pattern dialog.

2. Locate the appropriate matrix pattern file and highlight it.

3. Click Open.

To change method parameters:

1. Choose a matrix pattern by performing steps 1-3, above.

2. Double click on the method name in the Method Curtain; or select the method display, then select Analysis > Method Parameters.

3. Specify Threshold, taken as half of the average of the log-odds scores of sequences that were used to train the pattern. Increase the threshold for more stringency, decrease for more matches.

4. To select a different pattern, click Select Pattern File to return to the Matrix Pattern dialog.