*Other primer programs
Dan Jacobson
DANJ at JHUHYG.bitnet
Wed Jan 29 10:25:25 EST 1992
A request was made for information about PCR Primer programs other than the
one from the Whitehead institute. Well here's the readme file from the
other prgram availble over the net. I have no information about the commercial
programs.
Sincerely,
Dan Jacobson
danj at jhuhyg.sph.jhu.edu
=======================================================================
The program 'primer' is written by Don Faulkner. It helps to find potential
mispriming sites (primer sequences should be designed before running the
program!). The program allows to give higher weights to matches at the 3'
end of the primer, linearly decreasing them towards the 5' end (the default
is weight=10 for 3' nucleotide decreasing to 1 at nucleotide # 8 from the 3'
end). The program can be used when amplifying *long* fragments from a known
sequence.
The program is written in "C" and runs on Sun workstation (Unix).
To get the program running:
%ftp 36.45.0.126 or jmullins.stanford.edu
logon: anonymous
send your ID as a passwd
cd pub
set binary
get primer.tar
....
%tar xvf primer.tar
%make primer
%primer
... and you should get the sample run, presented below.
List of files:
-rw-rw-rw- 1 gene 532 Apr 8 18:33 Makefile
-rw-rw-rw- 1 gene 1527 Apr 8 17:25 backup.c
-rw-rw-rw- 1 gene 14226 Apr 8 17:16 clib.c
-rw-rw-rw- 1 gene 6174 May 7 1990 dynamic.c
-rw-rw-rw- 1 gene 208 May 7 1990 dynamic.h
-rw-rw-rw- 1 gene 2999 Apr 8 17:23 faulkn.h
-rw-rw-rw- 1 gene 208 May 7 1990 free.c
-rw-rw-rw- 1 gene 5328 May 7 1990 get-matrix.c
-rw-rw-rw- 1 gene 580 May 8 1990 hello.c
-rw-rw-rw- 1 gene 6679 Jun 5 1990 main.c
-rw-rw-rw- 1 gene 245 May 7 1990 matrix-test.c
-rw-rw-rw- 1 gene 8609 Apr 8 17:27 name-expander.c
-rw-rw-rw- 1 gene 1145 Apr 8 17:25 nread.c
-rw-rw-rw- 1 gene 4549 Apr 8 17:16 open_file.c
-rw-rw-rw- 1 gene 1629 May 11 1990 position-mat.c
-rw-rw-rw- 1 gene 8094 May 11 1990 rdseq.c
The file
-rw-r--r-- 1 gene 229 Apr 8 18:16 matrix
has the following:
actg ; this is the character set
match = 2
close = match / 2
missm = -match
;a c t g
match missm missm missm ;a
missm match missm missm ;c
missm missm match close ;t
missm missm close match ;g
These are sample files with several primer sequences and long template:
-rw-rw-rw- 1 gene 89 May 11 1990 3_primers
-rw-rw-rw- 1 gene 26769 May 11 1990 hxb-inv.seq
-rw-r--r-- 1 gene 40 Apr 8 17:31 .primer
Sample run is below:
%primer
*********************
* *
* DYNAMIC PRIMERS *
* *
*********************
Parameters for this search will be taken from
the previous one you made
OR you can specify new parameters.
Weighted search using the Dynamic Programming Algorighm
Gap Penalty, or <CR> for -2.000000 ->
LARGE sequence:
Enter name of file containing query
sequence, or <CR> for hxb-inv.seq ->
Locus names in the file <hxb-inv.seq>:
HXB2-INV
Enter locus name of query sequence, or <CR> for HXB2-INV ->
9719 bases found for locus HXB2-INV in file hxb-inv.seq
PRIMER sequence:
Enter name of file containing query
sequence, or <CR> for 3_primers ->
Locus names in the file <3_primers>:
sbc4
sbc5
sbc6
Enter locus name of query sequence, or <CR> for sbc4 ->
19 bases found for locus sbc4 in file 3_primers
Locus "HXB2-INV" (len = 9719) against "sbc4" (len = 19)
Position weighting matrix:
Default is Val=1 from 5' end to position (length-8)
linearly increasing to Val=10 at the 3' end of the primer.
If you want to CHANGE it enter 'y'
Output file:
File to write to -> test
2391 maxima
#1 score 95.875, 1 gap
4840 AATTTG-TTTTTGTAATTC
****. *.*******
1 CATTTTCCAATGGTAATTC
#2 score 95.125, 2 gaps
671 CAGCTGCC--TTGTAAGTC
**. *.** *.****.**
1 CATTTTCCAATGGTAATTC
#3 score 93.625, 4 gaps
5058 GATTGT---A-GGGAATTC
***.* * **.*****
1 CATTTTCCAATGGTAATTC
#4 score 93.625, 4 gaps
5008 AATTTT-C---TTTAATTC
***** * ..******
1 CATTTTCCAATGGTAATTC
#5 score 91.000, 3 gaps
8876 TTTTTTCCCATCGATCTAATTC
IT CHAR ****** ** * . ******
1 CATTTTCCAAT-G-G-TAATTC
#6 score 90.000, 5 gaps
1156 CCTCGTTACAATCAAGAGTAAGTC
* * .** **** * ****.**
1 CAT-TTTCCAAT---G-GTAATTC
#7 score 89.875, 3 gaps
1493 C-TTGCCCATTTATCTAATTC
* **. *** *. . ******
1 CATTTTCCAATG-G-TAATTC
#8 score 89.250, 4 gaps
6519 C-TGGT---GTGGTAAGTC
* *..* ******.**
1 CATTTTCCAATGGTAATTC
#9 score 87.500, 3 gaps
1577 C-TTGTGTAATTGTTAATTTC
* **.* ** **.*** ***
1 CATTTTCCAA-TGGTAA-TTC
#10 score 87.375, 4 gaps
6575 CTATGCTGCCCTATTTCTAAGTC
* **. *. ** **.. ***.**
1 C-ATT-TT-CCAATGG-TAATTC
#11 score 87.000, 5 gaps
2724 GAGTTGATACTACTGGCCTAATTC
* **. * * * *** ******
1 CA-TTT-T-CCAATGG--TAATTC
If you want to continue press 'y'
10 scores above threshold, 11 unique paths printed
Another PRIMER with sequence 'HXB2-INV' - press 'y'
If you want to INVERT the LARGE sequence - press 'i' i
Sequence 'HXB2-INV' has been inverted
PRIMER sequence:
Enter name of file containing query
sequence, or <CR> for 3_primers ->
Locus names in the file <3_primers>:
sbc4
sbc5
sbc6
Enter locus name of query sequence, or <CR> for sbc4 ->
19 bases found for locus sbc4 in file 3_primers
Locus "HXB2-INV_INVERTED" (len = 9719) against "sbc4" (len = 19)
Position weighting matrix:
Default is Val=1 from 5' end to position (length-8)
linearly increasing to Val=10 at the 3' end of the primer.
If you want to CHANGE it enter 'y'
Output file: test
File exists: Overwrite, Append, Reenter,
or Backup, or <CR> for Append ->
2372 maxima
#1 score 100.875, 0 gaps
7365 AATTTTTCTACTGTAATTC
***** * * .*******
1 CATTTTCCAATGGTAATTC
#2 score 93.500, 3 gaps
9082 GACTGG--AAGGGCTAATTC
* *.. **.** ******
1 CATTTTCCAATGG-TAATTC
#3 score 92.500, 5 gaps
4637 CA--GG--AATTTGGAATTC
** .. ** *.*.*****
1 CATTTTCCAA-TGGTAATTC
#4 score 89.625, 3 gaps
8043 C-TGTGCC--TTGGAATGC
* *.*.** *.*.***.*
1 CATTTTCCAATGGTAATTC
#5 score 89.500, 3 gaps
1 ---TGG--AAGGGCTAATTC
*.. **.** ******
1 CATTTTCCAATGG-TAATTC
#6 score 83.625, 4 gaps
8343 GAGTTAGGC-A-GGGATATTC
*.** . * * **.* ****
1 CATTT-TCCAATGGTA-ATTC
#7 score 81.375, 6 gaps
2235 C-TGTATCC---TTTAACTTC
* *.* *** ..*** ***
1 CATTT-TCCAATGGTAA-TTC
#8 score 80.500, 4 gaps
5347 CA--GACCAA--CTAATTC
** . **** ******
1 CATTTTCCAATGGTAATTC
#9 score 80.375, 6 gaps
2801 CAAGACTT-C--TGGGAAGTTC
* *. ** * ***.** ***
1 C-AT-TTTCCAATGGTAA-TTC
#10 score 80.000, 4 gaps
2099 CTGGCCTTCCTACAAGGGAAGGC
* .. **** * * **.**..*
1 CATT--TTCC-A-ATGGTAATTC
#11 score 79.125, 4 gaps
3335 AAATTG--AATTGGGCAAGTC
* **. ** ***. **.**
1 CATTTTCCAA-TGGT-AATTC
If you want to continue press 'y'
10 scores above threshold, 11 unique paths printed
Another PRIMER with sequence 'HXB2-INV_INVERTED' - press 'y'
If you want to INVERT the LARGE sequence - press 'i'
-------------- end of sample run ----------------------------
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