Jump to content

  • Log in with Facebook Log in with Twitter Log in with Windows Live Log In with Google      Sign In   
  • Create Account

Submit your paper to J Biol Methods today!
Photo
- - - - -

BLAST of ITS4 ITS5 sequence

blast its4 its5 fungus dna

  • Please log in to reply
2 replies to this topic

#1 wooz2002

wooz2002

    member

  • Members
  • Pip
  • 2 posts
0
Neutral

Posted 26 December 2011 - 06:54 AM

Hi, I have a question about BLASTing. Sequencing was done for a fungal strain. The PCR primers were ITS4 (reverse) and ITS5 (forward). I used the ITS4 sequence to BLAST and it gave a different results than the ITS5 BLAST; both results are quite close - results showed strain from the same genus; but the top result was different. Did I use BLAST wrongly? Or to rephrase the question, since I have one reverse sequence and one forward sequence, which should I use to BLAST or will need to do anything to the sequence before BLASTing? Thanks in advance!

#2 cbf88

cbf88

    member

  • Active Members
  • Pip
  • 14 posts
0
Neutral

Posted 26 December 2011 - 08:01 PM

I believe those primers are based on consensus and may not be an absolute perfect fit in all situations. Try starting with a search of one of the primers, then do a quick visual inspection for the reverse.

#3 Kamran

Kamran

    Kamran

  • Active Members
  • PipPipPipPipPip
  • 41 posts
2
Neutral

Posted 26 December 2011 - 10:18 PM

You should do Primer-BLAST (http://www.ncbi.nlm....s/primer-blast/). It will BLAST both of your forward and reverse primers simultaneously and would generate all possible results.





Home - About - Terms of Service - Privacy - Contact Us

©1999-2013 Protocol Online, All rights reserved.