Fungal refseq & data analysis

[nguyendofx]

Hello All,

I have large fungal sequence data sets (Illmina GA iix). I've been searching for Fungal reference sequence database. Does anyone know where to get most complete fungal refSeq? Is there any pipeline for fungal data analysis available? I would very appreciated it.

Thanks,
Ng

[GenoMax]

You may need to create a set based on what you need. I assume you are only interested in a specific sub-group of "fungi".

You will find fungal genomes at: http://fungi.ensembl.org/index.html and http://www.ncbi.nlm.nih.gov/genome/browse/ (change the "group" selection to fungi to filter out other eukaryotes).

[galloucf]

What fungi are you working with? We work with fungi and use several online databases that can be useful.

[nguyendofx]

Thanks genoMax and galloucf.

I am looking for the ITS region database instead of genomes, which is too much.

Thanks,
Ng

[krobison]

Perhaps this is in the mold of what you need

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2649129/

[nguyendofx]

Thanks krobison. I've got Nilsson's software. but its missing a ITS database.

[James Hane]

Hi Ng,

check out www.aftol.org, a large database of 6 conserved fungal regions including ITS sequences

Cheers,
James Hane

[ramsemm]

ITS or V9?

Hi,

I am fairly new to next-gen sequencing with most of my experience being with 16S-based studies. I am interested in looking at fungal diversity in soil rhizosphere samples, and I am wondering if V9 or the ITS region would be best to study? I see quite a few papers on the ITS region, but I have heard that previously the databases for this have not been ideal for this type of analysis.

I was wondering if anyone here might have suggestions as to which region (V9, ITS, or otherwise) is best to look at when examining fungal diversity and which database would you recommend using in the analysis?

Thanks in advance!