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Findley ITS Database

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The Segre Lab at NHGRI has provided the ITS database used in their Findley et al. 2013 Nature paper


ITS1 classification dataset v1

There are two data files in this distribution. The MD5 checksums are: MD5 (ITSdb.fasta) = e0e1e0c259da5268cbc8e95e5f9cf1bb MD5 (ITSdb.tax3) = 6a93fbc7332a3d61b985025929a355ee

ITSdb.fasta contains 23456 sequences of ITS1 sequences retrieved from Genbank in 2012. ITSdb.tax3 contains 23456 taxonomic strings, one per sequence. The strings are semicolon delimited:

Kingdom;Phylum;Class;Order;Family;Genus for example: Fungi;Basidiomycota;Basidiomycota_class_incertae_sedis;Malasseziales;Malasseziales_family_incertae_sedis;Malassezia;

These classification data were developed for use with the classify.seqs command in mothur (Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.).

For example:

classify.seqs(fasta=my.fasta,group=my.groups,template=ITSdb.fasta, taxonomy=ITSdb.tax3, method=knn, search=blast, match=2, mismatch=-2, gapopen=-2, gapextend=-1, numwanted=1)

Some of classification parameters (method=knn, search=blast, numwanted=1) should not be changed. The ITS1 sequence data were clustered at 95% identity using CD-HIT and may not work as expected for other methods (e.g., wang) or values of "numwanted". See the Methods and Supplemental Materials for Findley et al 2013 for details on how these data were generated and used.