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BaNG Nematode and Neglected Genomics |
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| The Blaxter Lab at the Institute of Evolutionary Biology, University of Edinburgh | ||
MOTU_define
Current version 2.07 released on 29th March 2007
Download Publications Feedback FAQs Change log Contact us If you are not sure what a MOTU is, please see the DNA Barcoding pages on our website.
This perl script, based on the ideas in CLOBB, uses blast-based similarity matching to define operational taxonomic units (MOTU) from DNA barcode data. It can use any sort of input data (COX1, SSU, LSU, etc). The discriminant level used for defining MOTU can be set by the user. The script now performs multiple cycles of OTU definition to test the robustness of the single-linkage clustering method employed.
2.07 is a major upgrade, in particular in that the software now produces a sensible summary of the analyses it has performed. Lots of other checks and balances have been added.
# In version 2.03 we changed the way the process labels sequences. It now places the MOTU number at the BEGINNING of the fasta header (>) line so 2.03 is INCOMPATIBLE with previous versions' databases, for which sorry, but it does mean that it is compatible with sequences downloaded as fasta files from GenBank or EMBL.
The download includes a small set of sequences to play with.
MOTU_define.pl is discussed and reviewed in the following publications
Floyd et al 2002 (download pdf)
Blaxter 2004 (download pdf)
Blaxter et al 2005 (download pdf)
...other interesting things... 
The rat hookworm Nippostrongylus brasiliensis. Hookworms are gut parasites of a wide range of vertebrates, including humans. This species is a rat parasite used as a research model for human hookworm disease. See NEMBASE3 for analyses of ESTs from this parasite and many other nematodes. |