Keith Seifert's Page

Keith Seifert replied to Conrad Schoch's discussion 'Definition of an acceptable Fungal ITS barcode' in the group Fungi

"Hi everyone, 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…"

Feb 15, 2012

Mike Trizna left a comment for Keith Seifert

"Keith, sorry to hear the poster upload didn't work. You're welcome to just e-mail the poster to cbol@si.edu and we'll upload it and link to it ourselves. Thanks for trying!"

Nov 18, 2011

Bryn T. M. Dentinger replied to Keith Seifert's discussion 'Defining the boundaries of the ITS barcode' in the group Fungi

"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…"

May 18, 2011

Henrik Nilsson replied to Keith Seifert's discussion 'Defining the boundaries of the ITS barcode' in the group Fungi

"Well in fact only one is non-fungal: >00062Mts_mtsctlts__Motse_J01871__X00525 (Mus musculus)"

May 18, 2011

Henrik Nilsson replied to Keith Seifert's discussion 'Defining the boundaries of the ITS barcode' in the group Fungi

">Keith said: >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…"

May 18, 2011

Bryn T. M. Dentinger replied to Keith Seifert's discussion 'Defining the boundaries of the ITS barcode' in the group Fungi

"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…"

May 17, 2011

Andrew Miller replied to Keith Seifert's discussion 'Defining the boundaries of the ITS barcode' in the group Fungi

"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…"

May 17, 2011

Keith Seifert added a discussion to the group Fungi

Defining the boundaries of the ITS barcode

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

May 17, 2011

5 Comments

Keith Seifert replied to Conrad Schoch's discussion 'Additional primers?' in the group Fungi

"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…"

Oct 26, 2010

Keith Seifert and BD Shenoy are now colleagues