This perl 5 script reads a DNA seq. from standard input, and writes to standard output the DNA with items plotted along the sequence. The 6 frame translation of the DNA seq. can be printed. Splice sites and polyA sites can be shown, as well as DNA features from an fplot format file.

The DNA code used for conceptual translation is eucaryotic. Stop codons are indicated in the output by '-'.

Usage: dna_plot [-aStart_bp,Stop bp -b# -d -f# -l -s -t Fplot.file] <DNA.file >DNA.plot


-aStart_bp,Stop_bp Translate only a subsequence between Start_bp and Stop_bp. The default is to translate the entire sequence.

-b# Bp per line in the output. Default is 50 bp for printing the translation and 60 bp when the translation is printed along with the DNA.

-d Print the translation along with the DNA.

-f# The DNA is only translated in the indicated reading frame.

-l Print the features only as dashes. The feature text won't be inserted

-s Print possible splice sites and polyA sites along the DNA.

-t Print the translation plotted along the DNA. By default, all 6 frames are printed. If -f# is used, a single frame can be specified.

If an fplot file is given, The fplot features are printed out along the DNA.

Example: dna_plot <DNA.file >DNA.translated Example: dna_plot -f1 <DNA.file >DNA.translated

Example: dna_plot -f-3 <DNA.file >DNA.translated Example: dna_plot -d <DNA.file >DNA.translated

Last updated 6-18-99 Written by Jim Lund in the lab of Roger Reeves, Johns Hopkins University