[EMBOSS] RE: prima

[Wei Tao]

Hi Sinead,

 

Thanks a lot for your quick response. I found a copy of prima in an older version of EMBOSS download.

 

My intention is to use prima for sequencing primer selection. However, after I tried a few sequences, from which I picked primers before, prima picked no forward sequencing primer at all. An example:

 

INPUT SUMMARY

*************

 

Prima of  from positions 50 to 600 bps

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 - 75.00 C

PRODUCT CONSTRAINTS:

Product GC content range is 0.40-0.55

Salt concentration is 50.00 (mM)

DNA concentration is 50.00 (nM)

Targeted range to amplify is from 50 to 600

 

 

PRIMER/PRODUCT PAIR CALCULATIONS & OUTPUT

 

Sequence is:

 

CCTATAGGGCGGCCGCGAATTCGGCACGAGGCTGCAACAGCAGACCAAGCACCGCGGCGGACCCAGGCAAGCACGGAACAAGCTGAGACGGATGATAATATGGATACAAAATCTATTCTAGAAGAACTTCTTCTCAAAAGATCACAGCAAAAG

AAGAAAATGTCACCAAATAATTACAAAGAACGGCTTTTTGTTTTGACCAAAACAAACCTTTCCTACTATGAATATGACAAAATGAAAAGGGGCAGCAGAAAAGGATCCATTGAAATTAAGAAAATCAGATGTGTGGAGAAAGTAAATCTCGAG

GAGCAGACGCCTGTAGAGAGACAGTACCCATTTCAGATTGTCTATAAAGATGGGCTTCTCTATGTCTATGCATCAAATGAAGAGAGCCGAAGTCAGTGGTTGAAAGCATTACAAAAAGAGATAAGGGGTAACCCCCACCTGCTGGTCAAGTAC

CATAGTGGGTTCTTCGTGGACGGGAAGTTCCTGTGTTGCCAGCAGAGCTGTAAAGCAGCCCCAGGATGTACCCTCTGGGAAGCATATGCTAATCTGCATACTGCAGTCAATGAAGAGAAACACAGAGTTCCCACCTTCCCAGACAGAGTGCTG

AAGATACCTCGGGCAGTTCCTGTTCTCAAAATGGATGCACCATCTTCAAGTACCACTCTAGCCCAATATGACAACGAATCAAAGAAAAACTATGGCTCCCAGCCACCATCTTCAAGTACCAGTCTAGCGCAATATGACAGCAACTCAAAGAAA

ATCTATGGCTCCCAGCCAAACTTCAACATGCAGTATATTCCAAGGGAAGACTTCCCTGACTGGTGGCAAGTAAGAAAA

 

 

Did you miss something in parameters? Any idea? Thanks again for your help.

 

Cheers, -Wei

 

 

 

 

-----Original Message-----
From: Sinéad O'Leary [mailto:oleary at genome.wi.mit.edu] 
Sent: Tuesday, September 02, 2003 1:39 PM
To: Wei Tao
Subject: Re: prima

 

Hi - I no longer work on the EMBOSS project but you can find any information and the latest downloads from the website below. I'm not sure if the prima program is still in the package, but there are another primer related programs called 'primers' and 'primersearch'. 

Version 2.7.0 is available from: 

    http://www.uk.embnet.org/Software/EMBOSS 
    ftp://ftp.uk.embnet.org/pub/EMBOSS 

There is an emboss mailing list where questions on any of the programs or installations are answered: <emboss at embnet.org> This may also be useful to you. 

hope this helps, 
Sinéad. 
  
  
  

Wei Tao wrote: 

	Hi Sinead,

	I wonder where can I find a copy of prima for download? Your help is deeply appreciated. 

	Thanks! 

	-Wei

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