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Programme for degenerate primer design


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9 replies to this topic

#1 thekid

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Posted 05 February 2009 - 01:50 PM

Hello,

I am looking at designing degenerate primers to detect between genotypes of viruses. I have to align around 1290 nucleotide sequences available in the genbank and then design primers based on the consensus seen.

Can anyone suggest me a program that will help me to do this.


the kid

#2 cellcounter

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Posted 05 February 2009 - 02:00 PM

Hello,

I am looking at designing degenerate primers to detect between genotypes of viruses. I have to align around 1290 nucleotide sequences available in the genbank and then design primers based on the consensus seen.

Can anyone suggest me a program that will help me to do this.


the kid

Look up the following search results for online tools and choose any one.
Primer Design Programs
Degenerate Primer Design

#3 bioforum

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Posted 05 February 2009 - 05:46 PM

Probably this is what you are looking for
PCR primers designed from protein multiple sequence alignments at http://blocks.fhcrc....ks/codehop.html

#4 fatema

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Posted 06 February 2009 - 03:13 AM

Hello,

I am looking at designing degenerate primers to detect between genotypes of viruses. I have to align around 1290 nucleotide sequences available in the genbank and then design primers based on the consensus seen.

Can anyone suggest me a program that will help me to do this.


the kid


Hi,

May I suggest you to have a look at AlleleID? AlleleID can design degenerate primers in the conserved region after identifying it using an alignment. This option is available in both the SYBR Green and TaqMan mode.

For details, please visit:
http://www.premierbi...tion/index.html

and request a key to use your own data if interested

Hope this helps.

Regards,
Fatema Sidhpurwala
PREMIER Biosoft International

#5 thekid

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Posted 06 February 2009 - 09:00 AM

Hello,

Thank you for the information. But I am looking for a software for aligning nearly 1000 nucleotide sequences and then designing the primers based on the alignment. So would like to know if this programme can do alignment for 1000 nucleotide sequences.

thekid

#6 enas

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Posted 17 February 2009 - 06:40 AM

Hello,

Thank you for the information. But I am looking for a software for aligning nearly 1000 nucleotide sequences and then designing the primers based on the alignment. So would like to know if this programme can do alignment for 1000 nucleotide sequences.

thekid



hey hi,
you can align your sequence here at this link :
http://blast.ncbi.nl...K_LOC=align2seq


and then ,after checking your primer you should use the whole seq and paste it on this link and it will give you your wanted primer :
http://frodo.wi.mit.edu/

#7 Springbok

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Posted 24 May 2009 - 12:01 AM

You should be able to do this in the latest version of Geneious Pro Geneious Home Page

#8 shane

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Posted 17 June 2010 - 09:45 PM

AlleleID can conceive degenerate primers in the conserved district after recognising it utilising an alignment. This choice is accessible in both the SYBR Green and TaqMan mode.

#9 bbrij87

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Posted 07 May 2011 - 03:30 PM

You can use AlleleID or genius pro. Both are good.

#10 Biouday

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Posted 11 December 2011 - 03:27 PM

You can also check
HYDEN - Software for Designing Degenerate Primers

http://lifescienceso...degenerate.html




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