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Finding the ITS region in my sequence


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#1 jdgriner

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Posted 19 November 2009 - 04:12 PM

I need to see if I can find the ITS region in my sequences. I have sequences from amplified 18s region and it is possible that I picked up the ITS region. How do I approach this problem? I don't know what to look for in my sequences. I am new to bioinformatics, and any help is appreciated.

#2 hobglobin

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Posted 20 November 2009 - 02:31 PM

I need to see if I can find the ITS region in my sequences. I have sequences from amplified 18s region and it is possible that I picked up the ITS region. How do I approach this problem? I don't know what to look for in my sequences. I am new to bioinformatics, and any help is appreciated.


A search with BLAST might help....if the ITS region of your organism is already in the database....

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...except casandra's that belong to the funniest, most interesting and imaginative (or over-imaginative?) ones, I suppose.

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#3 jdgriner

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Posted 20 November 2009 - 07:40 PM

I found out today that I need to find the paper that describes what exact regions that the SSU primers amplify. Medlin 1988 published a similar primer pair..Does anyone know what paper that is referenced in (SSU primers)?

#4 Adrian K

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Posted 22 November 2009 - 06:37 PM

Are you doing fungal research?
Expecting the world to treat you fairly because you are a good person is like expecting the lion not to attack you because you are a vegetarian.

..."best of our knowledge, as far as we know this had never been reported before, though I can't possible read all the published journals on earth, but by perform thorough search in google, the keywords did not match any documents"...

"what doesn't kill you, makes you stronger"---Goddess Casandra reminds me to be strong

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