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primer3-org / primer3

Primer3 is a command line tool to select primers for polymerase chain reaction (PCR).
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Could primer3 design primers based on alignment #56

Closed starsareintherose closed 2 years ago

starsareintherose commented 2 years ago

In the documents, I see, I can use multi templates in the file, such as so

SEQUENCE_ID=test1
SEQUENCE_TEMPLATE=GACTGATCGATGCTAGCTACGATCGATCGATGCATGCTAGCTAGCTAGCTGCTAGC
=
SEQUENCE_ID=test2
SEQUENCE_TEMPLATE=CATCATCATCATCGATGCTAGCATCNNACGTACGANCANATGCATCGATCGT
=
SEQUENCE_ID=test3
SEQUENCE_TEMPLATE=NACGTAGCTAGCATGCACNACTCGACNACGATGCACNACAGCTGCATCGATGC
=

But they produce separate results for themselves one by one, not considering them as alignment, or what should I do to design primers based on alignment My setting is here.

PIMER_TASK=generic
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_OPT_SIZE=20
PRIMER_MIN_SIZE=15
PRIMER_MAX_SIZE=26
PRIMER_MAX_NS_ACCEPTED=0
PRIMER_PRODUCT_SIZE_RANGE=500-600
SEQUENCE_EXCLUDED_REGION=500,900
PRIMER_EXPLAIN_FLAG=1
=
bioinfo-ut commented 2 years ago

Make a consensus sequence from alignment and use that as a template.

starsareintherose commented 2 years ago

But sometimes it is essential because we cannot always get a consensus sequence from alignment.

untergasser commented 2 years ago

Primer3 will only pick primers based on one input sequence. It is up to the user to provide this sequence. Primer3 does not create a consensus, as it only handles one sequence a time...

Best,

Andreas