There are a lot of issues brought up by different people in the discussion, so thanks for that.
What will happen at BOLD is that they will create an informatics pipeline that checks sequences submitted as ITS sequences to be sure that…"
"right, thanks for pointing out my taxonomic bias! looks like there is no universally constant region within the 28S that could serve as a handle without needing exceptions.
but rather than trimming sequences to within these motifs, what would be…"
>It will be helpful to establish a standard for ITS barcodes, and the proposal
>that I put on the table is that it be between these two motifs.
This sounds good to me. What about adding an additional requirement: that…"
"we have been routinely trimming our ITS sequences to beginning and ending with the CATTA- and -GACCT motifs. The -GACCT motif can vary a bit depending on which groups you work in (highly variable in Hygrocybe, for instance), but in my experience…"
"Good thoughts Keith.
My lab edits all ITS sequences to include the 5' and 3' primers. In most cases, this is ITS1F and ITS4 and would include your two proposed motifs above so I'm good with this.
If I'm not…"
Many people truncate their ITS sequences to begin with the last bases of the 18S, which facilitates alignment with some algorithms: CATTA The 28S begins with this set of bases in Saccharomyces, fairly conserved: GTTTGACCTCAAATCAGGTAGGAGTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGA It will be helpful to establish a standard for ITS barcodes, and the proposal that I put on the table is that it be between these two motifs. All of the ITS barcodes that are included in the data release for our paper should…See More
"At this stage, for data comparision, standardization of primers is probably not critical. But remember that standardization is a big deal in the barcoding world (practically the point of the whole thing actually), and in the end we will provide more…"
I’m involved in or interested in the following iBOL Working Groups
Keywords about my barcoding projects (separate each choice with a comma)
fungi, moulds, indoor mycota
I’m involved in the following aspects of barcoding:
Fieldwork/specimen collecting, Museum work/specimen curation, Labwork/generating barcode sequences, Management of barcode data, Analysis of barcode data, Using barcode data in taxonomy/systematic biology, Organizing/managing barcoding projects, Science policy related to barcoding
IM-BOL, Indoor Mycota Barcode of Life
I look happy in this picture because I am patting a koala!
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