[Leish-l] Index of mammal codes

[Kelly Harkins]

Hello everyone,

I have Illumina shotgun sequencing data for a number of Leishmania strains.
I'm about to upload the data on to NCBI/Sequence Read Archive and a couple
of the strains on to TriTrypDB.

I have WHO numbers for all.  Two of them, however, I am not familiar with
the mammal code and I cannot access this list on leishnet.net. Would anyone
be willing to share the index of mammal codes with me, or tell me what CEB
and DAS mammals refer to? I'm assuming DAS is Dasypus...


It might be of interest to this community that we used these shotgun data
to develop a bioinformatics approach that finds phylogenetically
informative sites within next-gen datasets when references or a priori
information aren't available. (http://arxiv.org/abs/1305.3665 for those
interested...). With the output for the *Leishmania *dataset, we designed
probes (manufactured by Mycroarray, MyBaits-2 kit) for targeted enrichment
that captures over 200,000 variable sites within 13,000 contigs from
genus-wide conserved regions. We also included probes in the design that
tile 3x across 42 genes, as well. We've only tested it initially with known
strains, L.V. braziliensis and a Crithidia sample; it appeared to work fine
preliminarily, i.e. the reads fell on their respective branch within the
phylogeny... I mention it here because perhaps this targeted enrichment
design will be of interest to someone in the field. Feel free to contact me
about it.

And, thank you for your help with the mammal codes,

Kelly M. Harkins, Ph.D.

Postdoctoral Scholar
UCSC Human Paleogenomics Lab
Department of Anthropology
University of California Santa Cruz
Santa Cruz, CA, 95064, USA
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