FRAMES⁽⁺⁾

Frames shows open reading frames for the six translation frames of a DNA sequence. Frames can superimpose the pattern of rare codon choices if you provide it with a codon frequency table.

Frames plots open reading frames of a nucleic acid sequence as boxes bordered by potential start and stop codons. Potential start codons are shown as short lines that extend above the box and potential stop codons are shown as short lines that extend below the box. By default, only the start and stop codons at the ends of open reading frames are shown in the frame display; if a stop codon has been passed, no stops are shown again until a start codon is passed; if a start codon is passed, no start codons are shown again until a stop codon is passed. You can display all start and stop codons with -ALL. Frames examines all six translation frames of a sequence.

If your sequence could have intervening sequences in it, use -ALL to get Frames to show all of the possible start and stop codons in your sequence.

If you know the pattern of codon usage in the system under study, Frames marks the occurrence of rare codons in each reading frame. Use Codon Frequency Table to have the rare codons marked. If you want to use a codon frequency file other than ecohigh.cod, you can specify this file with Codon Frequency Table set to codontablename.cod.

If you are reading the Program Manual, the output from this session and from another session with -ALL are shown in the two figures at the end of this program entry. In the first figure showing open reading frames, potential start codons are indicated by lines extending above the reading frame box and stop codons are indicated by lines extending below the box. In the second figure showing all potential start and stop codons, potential start codons are indicated by vertical lines above the horizontal and stop codons are indicated by vertical lines below the horizontal. In both plots, the positions of rare codons are indicated by dots above each translation frame.

Frames accepts as input a single nucleotide sequence. If Frames rejects your nucleotide sequence, turn to Appendix VI to see how to change or set the type of a sequence.

Map can display the translation of open reading frames of a sequence. CodonPreference, TestCode, and Window/StatPlot help to identify coding regions. FitConsensus searches for consensus sequences.

Frames treats all the frames as open at the beginning of each strand in the range you have chosen. This could be misleading.

You can set the parameters listed below from the command line. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.

Translation Table Select From List

Usually, the Standard translation table is the basis for all translations. You can choose translation tables for various non-standard genomes such as yeast mitochondrial.

Show all start and stop signals, not just open frames

makes Frames show all of the potential starts and stops regardless of what precedes them in the sequence.

Codon Frequency Table Select From List

If you use this parameter, Frames uses a codon frequency file of the kind written by CodonFrequency and a threshold at or below which you want to have the rare codons marked. Then, when Frames passes a codon whose value in column five of the codon frequency table falls at or below your threshold setting, the plot is marked with a dot above the codon.

Threshold at or below which rare codons are shown

sets the threshold at or below which rare codons are shown in the plot. When Frames passes a codon whose value in column five of the codon frequency table falls at or below your threshold setting, the plot is marked with a dot above the codon.

Printed: January 13, 1999 6:27 (1162)

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