PRIMO
A primer design tool
Kupfer, Li
P. Li, K. C. Kupfer, C. J. Davies, D. Burbee, G. A. Evans, and H. R. Garner. PRIMO: A primer design program that applies base quality statistics for automated large-scale DNA sequencing. Genomics 40:476-485 (1997).
primo
primo
perl
"primo"
0
input_file_name
Sequence data
perl
" $value"
8
1
all
perl
" -all"
10
cover
cover template with walking-primers on both strands (-cover)
perl
($value)? " -cover" : ""
10
print
perl
! $cover
print formatted/annotated sequence to log file (-print)
perl
($value)? " -print" : ""
10
regions_file
Regions file (-read)
perl
($value)? " -read $input_file_name" : ""
10
qual_file
Quality datafile file
perl
($value)? "" : " -noqual"
10
repeats_file
Repeats file
perl
($value)? "ln -s $value human.rep; " : ""
-10
See the file http://bioweb.pasteur.fr/docs/doc-gensoft/primo/example//human.rep.bac for an example.
oligo_file
Oligo file
Name Oligo\noligo1 GAGGCAGGAGAATGGCAC
perl
($value)? "ln -s $value oligo.screen; " : ""
-10
rf
perl
$regions_file
perl
"ln -s $regions_file $input_file_name.regions; "
-10
qf
perl
$qual_file
perl
"ln -s $qual_file $input_file_name.qual; "
-10
results_files
*.log *.primers oligo.cri