In article <930302110524.2051 at VTHVAX.TAMU.EDU> MCAO at VTHVAX.TAMU.EDU writes:
>Hi, Do you know where to get this kind of software from public domain? I would like to get one for primer design.
>> Ming Cao
>
There are, to my knowledge 4 programs which deal with pcr primer
construction which one can obtain by anonymous ftp and one which
will be mailed to you by the author.
The programs are listed below in no particular order.
Pgen - for Dos only
Primer - Stanford - Sun Sparcstations only
Primer - Whitehead -Unix, Vms, DOS (and Mac if you can compile it)
Amplify - Mac only
OSP - Unix, X-windows, Vms, DOS, Mac - by snail-mail only.
Below is all the info I have on said programs.
Hope this helps,
Dan Jacobson
Kudos go to the authors and the ftp site maintainers.
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Pgen
An excerpt from the PrimerGen's documentation:
PrimerGen searches strings of amino acid residues in order to reverse-translate
oligonucletide primers of a desired range of lengths and maximum number of
degeneracies.
PrimerGen only works on IBM-PC(TM), XT, AT, PS/2 and compatibles with
EGA or VGA graphics adaptors. It will not work on computers with CGA or
Hercules(TM) graphics cards. This is because the program alters the
screen fonts which cannot be done on the latter types of graphics
adaptors. I have no access to XGA card-driven computers, so I don't
know what happens there! A hard drive is NOT required and PrimerGen will
fit on a 360K 5.25" floppy disk.
You need to input:
- the appropriate amino acid sequence,
- the minimum size of desired primers,
- the maximum size of primers (important for codon preference -
generated primers),
- the maximum acceptable number of mismatches,
- desired codon preference table (if required).
The program will also supply the melting temperature of the primer. You may
input the Na or K cation concentration used in the melting temperature
calculations.
PrimerGen contains a sequence editor, where amino acid residues are entered.
The amino acid sequence must be ONE fragment and cannot be longer than 70
residues. The sequence must be in the ONE LETTER CODE and cannot contain
any UNKNOWNS. After the desired amino acid sequence has been entered have the
option of saving the sequence to a disk. PrimerGen will also accept and
re-edit previously saved sequence files, and also contains a codon preference
table editor.
anonymous ftp from ftp.bio.indiana.edu in the molbio/ibmpc directory.
============================================================================
////////////////////////////////////////////////////////////////////////////
============================================================================
Priner - Stanford
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 g
