primer3 does not output complete primer name if only choosing left or right primers

[Robert Citek]

Binary package hint: primer3

When designing only left or right primers, primer3 does output the full output tag name for the primer when the input tag PRIMER_NUM_RETURN= goes to 11 (or higher.)

$ cat /etc/lsb-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=7.10
DISTRIB_CODENAME=gutsy
DISTRIB_DESCRIPTION="Ubuntu 7.10"

$ dpkg -l primer3
Desired=Unknown/Install/Remove/Purge/Hold
| Status=Not/Installed/Config-f/Unpacked/Failed-cfg/Half-inst/t-aWait/T-pend
|/ Err?=(none)/Hold/Reinst-required/X=both-problems (Status,Err: uppercase=bad)
||/ Name Version Description
+++-=================================-=================================-==================================================================================
ii primer3 1.1.1-1 Tool to design flanking oligo nucleotides for DNA amplification

$ cat example.n11.input
PRIMER_SEQUENCE_ID=example
SEQUENCE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
TARGET=37,21
PRIMER_OPT_SIZE=18
PRIMER_MIN_SIZE=15
PRIMER_MAX_SIZE=21
PRIMER_NUM_NS_ACCEPTED=1
PRIMER_FILE_FLAG=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_NUM_RETURN=11
PRIMER_TASK=pick_left_only
=

$ primer3_core < example.n11.input | tail -20
PRIMER_LEFT_8_SELF_ANY=5.00
PRIMER_LEFT_8_SELF_END=2.00
PRIMER_LEFT_8_END_STABILITY=7.8000
PRIMER_LEFT_9_PENALTY=1.8066
PRIMER_LEFT_9_SEQUENCE=TCCCGACCCAAATCGATAG
PRIMER_LEFT_9=78,19
PRIMER_LEFT_9_TM=60.807
PRIMER_LEFT_9_GC_PERCENT=52.632
PRIMER_LEFT_9_SELF_ANY=6.00
PRIMER_LEFT_9_SELF_END=2.00
PRIMER_LEFT_9_END_STABILITY=5.6000
_10_PENALTY=1.8114
_10_SEQUENCE=TCGATCCCGACCCAAATC
_10=74,18
_10_TM=61.811
_10_GC_PERCENT=55.556
_10_SELF_ANY=4.00
_10_SELF_END=0.00
_10_END_STABILITY=6.9000
=

[Robert Citek (robert-citek)]

I've contacted the developers at Sourceforge:

http://primer3.sourceforge.net/

From one of the developers:

<quote>
I am pretty sure I know what the problem is,
since I just found it myself a week ago,

I tagged a release-1.1.3 in svn that
I think fixes the bug (I need to test on my home machine,
where the bug shows up). If you are able
to checkout this release from svn and confirm
that the bug is gone, that would help.
</quote>

[Robert Citek (robert-citek)]

Version 1.1.3 has the bug fix.

$ svn co https://primer3.svn.sourceforge.net/svnroot/primer3/primer3/tags/release-1.1.3

$ cd release-1.1.3/src/

$ make all

$ make test

$ echo 'PRIMER_NUM_RETURN=11
PRIMER_TASK=pick_left_only
SEQUENCE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
=' | ./primer3_core | tail -20

PRIMER_LEFT_8_SELF_ANY=2.00
PRIMER_LEFT_8_SELF_END=2.00
PRIMER_LEFT_8_END_STABILITY=6.9000
PRIMER_LEFT_9_PENALTY=1.7978
PRIMER_LEFT_9_SEQUENCE=CACACACACACAGCACACAG
PRIMER_LEFT_9=39,20
PRIMER_LEFT_9_TM=58.202
PRIMER_LEFT_9_GC_PERCENT=55.000
PRIMER_LEFT_9_SELF_ANY=2.00
PRIMER_LEFT_9_SELF_END=1.00
PRIMER_LEFT_9_END_STABILITY=6.7000
PRIMER_LEFT_10_PENALTY=1.8066
PRIMER_LEFT_10_SEQUENCE=TCCCGACCCAAATCGATAG
PRIMER_LEFT_10=78,19
PRIMER_LEFT_10_TM=60.807
PRIMER_LEFT_10_GC_PERCENT=52.632
PRIMER_LEFT_10_SELF_ANY=6.00
PRIMER_LEFT_10_SELF_END=2.00
PRIMER_LEFT_10_END_STABILITY=5.6000
=

$ echo 'PRIMER_NUM_RETURN=1000
PRIMER_TASK=pick_left_only
SEQUENCE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
=' | ./primer3_core | tail -20

PRIMER_LEFT_70_SELF_ANY=3.00
PRIMER_LEFT_70_SELF_END=2.00
PRIMER_LEFT_70_END_STABILITY=5.7000
PRIMER_LEFT_71_PENALTY=8.4850
PRIMER_LEFT_71_SEQUENCE=CACACACACAGCACACAGGTATTAGT
PRIMER_LEFT_71=41,26
PRIMER_LEFT_71_TM=62.485
PRIMER_LEFT_71_GC_PERCENT=46.154
PRIMER_LEFT_71_SELF_ANY=3.00
PRIMER_LEFT_71_SELF_END=2.00
PRIMER_LEFT_71_END_STABILITY=5.7000
PRIMER_LEFT_72_PENALTY=8.4850
PRIMER_LEFT_72_SEQUENCE=ACACACACACAGCACACAGGTATTAG
PRIMER_LEFT_72=40,26
PRIMER_LEFT_72_TM=62.485
PRIMER_LEFT_72_GC_PERCENT=46.154
PRIMER_LEFT_72_SELF_ANY=3.00
PRIMER_LEFT_72_SELF_END=1.00
PRIMER_LEFT_72_END_STABILITY=5.9000
=

Looks good. Now the question is, what needs to happen to get it packaged and in the repositories?

[Robert Citek (robert-citek)]

Works with the primer3-1.1.3-candidate release.

http://sourceforge.net/project/showfiles.php?group_id=112461&package_id=211061&release_id=578504

$ tar -xzvf primer3-1.1.3.tar.gz

$ cd primer3-1.1.3/src/

$ make all && make test

$ echo 'PRIMER_NUM_RETURN=11
PRIMER_TASK=pick_left_only
SEQUENCE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
=' | ./primer3_core | tail -20

PRIMER_LEFT_8_SELF_ANY=2.00
PRIMER_LEFT_8_SELF_END=2.00
PRIMER_LEFT_8_END_STABILITY=6.9000
PRIMER_LEFT_9_PENALTY=1.7978
PRIMER_LEFT_9_SEQUENCE=CACACACACACAGCACACAG
PRIMER_LEFT_9=39,20
PRIMER_LEFT_9_TM=58.202
PRIMER_LEFT_9_GC_PERCENT=55.000
PRIMER_LEFT_9_SELF_ANY=2.00
PRIMER_LEFT_9_SELF_END=1.00
PRIMER_LEFT_9_END_STABILITY=6.7000
PRIMER_LEFT_10_PENALTY=1.8066
PRIMER_LEFT_10_SEQUENCE=TCCCGACCCAAATCGATAG
PRIMER_LEFT_10=78,19
PRIMER_LEFT_10_TM=60.807
PRIMER_LEFT_10_GC_PERCENT=52.632
PRIMER_LEFT_10_SELF_ANY=6.00
PRIMER_LEFT_10_SELF_END=2.00
PRIMER_LEFT_10_END_STABILITY=5.6000
=

$ echo 'PRIMER_NUM_RETURN=1000
PRIMER_TASK=pick_left_only
SEQUENCE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
=' | ./primer3_core | tail -20

PRIMER_LEFT_70_SELF_ANY=3.00
PRIMER_LEFT_70_SELF_END=2.00
PRIMER_LEFT_70_END_STABILITY=5.7000
PRIMER_LEFT_71_PENALTY=8.4850
PRIMER_LEFT_71_SEQUENCE=CACACACACAGCACACAGGTATTAGT
PRIMER_LEFT_71=41,26
PRIMER_LEFT_71_TM=62.485
PRIMER_LEFT_71_GC_PERCENT=46.154
PRIMER_LEFT_71_SELF_ANY=3.00
PRIMER_LEFT_71_SELF_END=2.00
PRIMER_LEFT_71_END_STABILITY=5.7000
PRIMER_LEFT_72_PENALTY=8.4850
PRIMER_LEFT_72_SEQUENCE=ACACACACACAGCACACAGGTATTAG
PRIMER_LEFT_72=40,26
PRIMER_LEFT_72_TM=62.485
PRIMER_LEFT_72_GC_PERCENT=46.154
PRIMER_LEFT_72_SELF_ANY=3.00
PRIMER_LEFT_72_SELF_END=1.00
PRIMER_LEFT_72_END_STABILITY=5.9000
=

[Robert Citek (robert-citek)]

Here's a script which automates the above:

true && (

set -x

wget 'http://superb-west.dl.sourceforge.net/sourceforge/primer3/primer3-1.1.3.tar.gz'

tar -xzvf primer3-1.1.3.tar.gz

cd primer3-1.1.3/src/

make all

make test

echo 'PRIMER_NUM_RETURN=11
PRIMER_TASK=pick_left_only
SEQUENCE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
=' | ./primer3_core | tail -20

echo 'PRIMER_NUM_RETURN=1000
PRIMER_TASK=pick_left_only
SEQUENCE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
=' | ./primer3_core | tail -20

) 2>&1 | tee output.txt

[Robert Citek (robert-citek)]

I had to modify the script to get it to work under Solaris:

$ uname -srvmpi
SunOS 5.10 Generic_118822-10 sun4u sparc SUNW,Sun-Fire-V490

The modified script (seems to be more general as it works in Ubuntu, too):

true && (

set -x

wget 'http://superb-west.dl.sourceforge.net/sourceforge/primer3/primer3-1.1.3.tar.gz'

gunzip -c primer3-1.1.3.tar.gz |
tar -xvf -

find primer3-1.1.3 -name 'Makefile' |
xargs -i dos2unix {} {}

cd primer3-1.1.3/src/

make all

make test

echo 'PRIMER_NUM_RETURN=11
PRIMER_TASK=pick_left_only
SEQUENCE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
=' | ./primer3_core | tail -20

echo 'PRIMER_NUM_RETURN=1000
PRIMER_TASK=pick_left_only
SEQUENCE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
=' | ./primer3_core | tail -20

) 2>&1 | tee output.txt

[Charles Plessy (plessy)]

This bug has been solved in version 1.1.3-1.

Have a nice day,

--
Charles Plessy
Debian Med packaging team
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan