CSC

find_primers

This command performs the Gap4 "Suggest Primers" function. It searches for locations where choosing an oligo primer for "walking" off another reading will solve a problem. The command returns a list of primer information in the form "template_name reading_name primer_identifier sequence position direction", separated by newlines.

find_primers
 -io            io_handle:integer
 -contigs       identifiers:strings()
?-search_from   position:integer(20)?
?-search_to     position:integer(60)?
?-num_primers   count:integer(1)?
?-primer_start  count:integer(1)?
?-params        OSP_params:string?

-io io_handle

The database IO handle returned from a previous open_db call.

-contigs identifiers

This specifies the list of contigs to search. The {contig start end} syntax may be used for an identifier to search only a region of the contig, otherwise all of it is searched.

-search_from position

-search_to position

These two options control the region, relative to the problem, in which to look for suitable oligos. The defaults are from 20 to 60, which means that to cover an area starting at position 1000 in the forward strand the command will pick oligos from the sequence at positions 940 to 980.

-num_primers count

This controls how many oligos to pick to solve each problem. The default is 1.

-primer_start count

Each oligo is given a primer name consisting of the database name followed by the primer number. The numbers start at count and increment for each new primer. The default is 1.

-params OSP_params

This specifies the parameters to the OSP algorithm as a keyed list. The defaults are undefined unless the gaprc file has been parsed. In this case the defaults are as used by Gap4. Not all of the OSP parameters listed below are needed or used, but we don't have further details. The defaults listed in the gaprc file are:

#----------------------------------------------
# The OSP Prm defaults
#----------------------------------------------
set_def OSP.prod_len_low                0
set_def OSP.prod_len_high               200
set_def OSP.prod_gc_low                 0.40
set_def OSP.prod_gc_high                0.55
set_def OSP.prod_tm_low                 70.0
set_def OSP.prod_tm_high                90.0

set_def OSP.min_prim_len                17
set_def OSP.max_prim_len                23
set_def OSP.prim_gc_low                 0.30
set_def OSP.prim_gc_high                0.70
set_def OSP.prim_tm_low                 50
set_def OSP.prim_tm_high                55

set_def OSP.self3_hmlg_cut              8
set_def OSP.selfI_hmlg_cut              14
set_def OSP.pp3_hmlg_cut                8
set_def OSP.ppI_hmlg_cut                14
set_def OSP.primprod3_hmlg_cut          0
set_def OSP.primprodI_hmlg_cut          0
set_def OSP.primother3_hmlg_cut         0.0
set_def OSP.primotherI_hmlg_cut         0.0
set_def OSP.delta_tm_cut                2.0
set_def OSP.end_nucs                    S

set_def OSP.wt_prod_len                 0
set_def OSP.wt_prod_gc                  0
set_def OSP.wt_prod_tm                  0
set_def OSP.wt_prim_s_len               0
set_def OSP.wt_prim_a_len               0
set_def OSP.wt_prim_s_gc                0
set_def OSP.wt_prim_a_gc                0
set_def OSP.wt_prim_s_tm                0
set_def OSP.wt_prim_a_tm                0
set_def OSP.wt_self3_hmlg_cut           2
set_def OSP.wt_selfI_hmlg_cut           1
set_def OSP.wt_pp3_hmlg_cut             2
set_def OSP.wt_ppI_hmlg_cut             1
set_def OSP.wt_primprod3_hmlg_cut       0
set_def OSP.wt_primprodI_hmlg_cut       0
set_def OSP.wt_primother3_hmlg_cut      0
set_def OSP.wt_primotherI_hmlg_cut      0
set_def OSP.wt_delta_tm_cut             0
set_def OSP.AT_score                    2
set_def OSP.CG_score                    4
set_def OSP.wt_ambig                    avg

To change a default you need to specify the full OSP parameters with modified values. For instance:

global gap_defs

set osp_defs [keylget gap_defs OSP]
keylset osp_defs min_prim_len 18

find_primers \
        -params $osp_defs \
        (etc)