EMBOSS: prima

Program prima

Function

Selects primers for PCR and DNA amplification

Description

Usage

Here is a sample session with prima. 

% prima
Input sequence: embl:eclaci
Specify a Target Range? [N]: 
Minimum Primer Tm (deg Celsius) [53]: 
Maximum Primer Tm (deg Celsius) [58]: 
Minimum product length [100]: 
Maximum product length [300]: 
Output file [eclaci.prima]:

Command line arguments 

   Mandatory qualifiers (* if not always prompted):
  [-sequence]          sequence   Sequence USA
  [-targetrange]       bool       Specify a Target Range?
*  -targetstart        integer    Target start position.
*  -targetend          integer    Target end position.
   -minprimertm        float      Minimum Primer Tm (deg Celsius)
   -maxprimertm        float      Maximum Primer Tm (deg Celsius)
*  -minprodlen         integer    Minimum product length
*  -maxprodlen         integer    Maximum product length
  [-outf]              outfile    Output file name

   Optional qualifiers: (none)
   Advanced qualifiers:
   -overlap            integer    Minimum overlap of sequences
   -minprimerlen       integer    Minimum primer length
   -maxprimerlen       integer    Minimum primer length
   -minpmgccont        float      Minimum primer GC fraction
   -maxpmgccont        float      Maximum primer GC fraction
   -minprodgccont      float      Minimum product GC fraction
   -maxprodgccont      float      Maximum product GC fraction
   -saltconc           float      Salt concentration (mM)
   -dnaconc            float      DNA concentration (mM)
   -list               bool       Force list-style output

Mandatory qualifiers Allowed values Default
[-sequence]
(Parameter 1)		 Sequence USA Readable sequence Required
[-targetrange]
(Parameter 2)		 Specify a Target Range? Yes/No No
-targetstart Target start position. Any integer value Start of sequence
-targetend Target end position. Any integer value End of sequence
-minprimertm Minimum Primer Tm (deg Celsius) Any integer value 53
-maxprimertm Maximum Primer Tm (deg Celsius) Any integer value 58
-minprodlen Minimum product length Any integer value 100
-maxprodlen Maximum product length Any integer value 300
[-outf]
(Parameter 3)		 Output file name Output file <sequence>.prima
Optional qualifiers Allowed values Default
(none)
Advanced qualifiers Allowed values Default
-overlap Minimum overlap of sequences Any integer value 50
-minprimerlen Minimum primer length Any integer value 18
-maxprimerlen Minimum primer length Any integer value 22
-minpmgccont Minimum primer GC fraction Number from 0.300 to 0.700 .40
-maxpmgccont Maximum primer GC fraction Number from 0.300 to 0.700 .55
-minprodgccont Minimum product GC fraction Number from 0.300 to 0.700 .40
-maxprodgccont Maximum product GC fraction Number from 0.300 to 0.700 .55
-saltconc Salt concentration (mM) Number from 1.000 to 100.000 50
-dnaconc DNA concentration (mM) Number from 1.000 to 100.000 50
-list Force list-style output Yes/No No

Input file format

Output file format

Here is the output from the example run: 




INPUT SUMMARY
*************

Prima of ECLACI
PRIMER CONSTRAINTS:
PRIMA DOES NOT ALLOW PRIMER SEQUENCE AMBIGUITY OR DUPLICATE PRIMER ENDPOINTS
Primer size range is 18-22
Primer GC content range is 0.40-0.55
Primer melting Temp range is 53.00 - 58.00 C
PRODUCT CONSTRAINTS:
Product GC content range is 0.40-0.55
Salt concentration is 50.00 (mM)
DNA concentration is 50.00 (nM)
Considering all suitable Primer pairs with Product length ranges 100 to 300




PRIMER/PRODUCT PAIR CALCULATIONS & OUTPUT
*****************************************

3 pairs found


                Forward                                 Reverse

[1]
    10 AGTCAATTCAGGGTGGTGAA      29        154 ATGTAATTCAGCTCCGCCAT      173
       Tm  56.24 C  (GC 50.00%)                Tm  57.14 C  (GC 50.00%)
             Length: 20                              Length: 20
             Tma:    40.56 C                         Tma:    40.83 C


       Product GC: 53.23%
       Product Tm: 55.12 C
       Length:     124


[2]
   266 TTGTCGCGGCGATTAAATCTC     286       510 GTACCGTCTTCATGGGAGAAA     530
       Tm  57.88 C  (GC 42.86%)                Tm  55.78 C  (GC 42.86%)
             Length: 21                              Length: 21
             Tma:    42.45 C                         Tma:    41.82 C


       Product GC: 54.71%
       Product Tm: 57.13 C
       Length:     223


[3]
   477 TGTCTCTGACCAGACACCC       495       728 GGAACGATGCCCTCATTCA       746
       Tm  54.99 C  (GC 52.63%)                Tm  55.20 C  (GC 52.63%)
             Length: 19                              Length: 19
             Tma:    42.28 C                         Tma:    42.34 C


       Product GC: 53.02%
       Product Tm: 58.12 C
       Length:     232

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also
Program nameDescription
primersearchSearches DNA sequences for matches with primer pairs
stssearchSearches a DNA database for matches with a set of STS primers

Author(s)

This application was written by Sinead O'Leary (soleary@hgmp.mrc.ac.uk)

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments