Database will be used to analyze environmental samples. Metagenomic DNA sequences obtained through illumina.
Curated databases for fungal (I guess also for other microbes) are highly desired. Currently, rDNA ITS sequences can be analyzed / compared with MycoID (at MycoBank) and UNITE databases, which are both specimen-based and curated.
MycoID: http://www.mycobank.org/
UNITE: http://unite.ut.ee/
MycoID database contains also other DNA sequences such as rDNA LSU, rDNA SSU, RPB1, B-Tub, TEF-1, and some more.
For DNA or incomplete genome sequence, see Andrey's response, otherwise ...
If by 'genome' you mean completely-sequenced, then there is a well-maintained list of proteomes of completely sequenced organisms here:
http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/taxonomic_gen_list.cgi#model_Fungi
with strains of the same species here:
http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/taxonomic_gen_list.cgi#strain_Fungi
And if by 'curated' you mean protein domain annotations, then you will find that by clicking on the links for the individual genomes. There are also very many comparative genomics tools, and in your case you might find it interesting that there are hundreds of meta-genomic environmental samples for comparison here:
http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/gen_list.cgi#meta
If you want us to upload and/or analyse your data, get in touch!
I know this one. Hope it helps.
http://genome.jgi.doe.gov/programs/fungi/index.jsf
Thank you very much for your responses. I am evaluating which database will be more useful to incorporate into out pipeline. Will update you on which one worked best when the data gets analyzed.
for whole genome there is no database and actually there is whole genome sequences just for a few fungi. But for partial sequences you can search NCBI.
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