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PRIMA : Selects primers for PCR and DNA amplification. (EMBOSS)



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( = required, = conditionally required)


input Section


required Section


advanced Section

Minimum overlap of sequences (-overlap)
Salt concentration (mM) (-saltconc)
DNA concentration (mM) (-dnaconc)
Force list-style output (-list)

output Section


input Section


sequence [single sequence] (-sequence) : please enter
either :
  1. the name of a file:
  2. or the actual data here:

(sequence format)


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required Section

Specify a Target Range? (-targetrange)
Minimum Primer Tm (deg Celsius) (-minprimertm)
Maximum Primer Tm (deg Celsius) (-maxprimertm)

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advanced Section


targetrangesection Section


primer Section


product Section


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targetrangesection Section

Target start position. (-targetstart)
Target end position. (-targetend)

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primer Section

Minimum primer length (-minprimerlen)
Maximum primer length (-maxprimerlen)
Minimum primer GC fraction (-minpmgccont)
Maximum primer GC fraction (-maxpmgccont)

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product Section

Minimum product length (-minprodlen)
Maximum product length (-maxprodlen)
Minimum product GC fraction (-minprodgccont)
Maximum product GC fraction (-maxprodgccont)

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output Section

outf (-outf)

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Some explanations about the options


input Section
enter either the name of a file or the actual data
if you are using Netscape 2.x or later, you can select a file by typing its name, or better, by selecting it with the Netscape file browser (Browse button)
OR you can type your data in the next area, or cut and paste it from another application.
(but not both)
Sequence format
The sequence will be automatically converted in the format needed for the program
providing you enter a sequence either:
in plain (raw) sequence format or in one of the following known formats:
IG,GenBank,NBRF,EMBL,GCG,DNAStrider,Fitch,fasta,Phylip,PIR,MSF,ASN,PAUP,CLUSTALW
You may enter in the text area a database entry code, or an accession number, in this form:
database:entry_name
or:
database:accession.

Pise form generator version: 5.a (11 Nov 2002 10:21)