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Primer3 and Blast


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3 replies to this topic

#1 amv33576

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Posted 26 January 2011 - 03:44 PM

Hello!

I am wondering, if is there a way to run on a local database, Primer3 and Blast like is performed online?

Thanks in advance.

#2 Radish

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Posted 26 January 2011 - 09:54 PM

Hello!

I am wondering, if is there a way to run on a local database, Primer3 and Blast like is performed online?

Thanks in advance.

yes, get your PI to buy vector NTI.
The software allows you to create your own database, annotate it anyway you like and it as several design tools (siRNAs, primers, restriction sites etc)

Best regards

Radish

#3 HomeBrew

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Posted 27 January 2011 - 01:44 AM

You needn't buy anything. Primer3 and the stand-alone BLAST programs are all open source, and are all you need. Pre-compiled BLAST databases are available for download from NCBI, or you can make your own by running a compilation of sequences in FASTA format through one of the BLAST utilities (formatdb).

#4 Radish

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Posted 27 January 2011 - 08:38 AM

It depends, if you are looking for cryptic exons or conserved intronic regions it gets really hard to work with primer3+blast

And you have lots of other opensource tools. I just suggested vector NTI because from all the tools that I tried it was the closest to user friendly.

My writing didn't convey my thoughts LOL, vector NTI is definitely not the only fish in the sea but sure is tasty!

Best regards
Radish




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