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Overview

The bushmeat trade in tropical Africa represents illegal, unsustainable off-takes of millions of tons of wild game —mostly mammals— per year. Because the bushmeat items sold on markets may consist of unrecognizable pieces of processed meat, we provide a species-identification genetic tool (how to) based on ‘forensically informative nucleotide sequencing’ (FINS) to complement standard bushmeat surveys. Our expert-curated nucleotide datasets shall be progressively fed to become a reference framework for the DNA-typing of African forest bushmeat.

Material

At the moment, DNAbushmeat is composed of four queriable nucleotide datasets representing four mtDNA genes (cytochrome b, cytochrome oxidase I, 12S and 16S) and 60 species of mammals from African rainforest. The four gene fragments are straightforward to amplify via a protocol using single, ‘universal’ primer pairs that appeared robust to different types of meat pre-processing and DNA extraction protocols. The usefulness of our multi-locus approach in reaching bushmeat species identification was assessed using a decision pipeline combining similarity- and tree-based approaches with an assessment of taxonomic expertise and coverage of Genbank sequences (Gaubert et al. in press).




Required field icon required conditionally required optional


Fasta sequence file : please enter either :
  1. Select a file:
  2. or paste your fasta sequence here:


1e-

Type of model





Top

Some explanations about the options


How to identify my mtDNA sequence(s)?

  1. Generate nucleotide sequences corresponding to the fragments of cytochrome b, cytochrome oxidase I, 12S and 16S used in Gaubert et al. (in press).
  2. Paste your sequence in the data field or attach your sequence file (fasta format) for a local blast in the four reference datasets (cytochrome b, cytochrome oxidase I, 12S and 16S). Note that the different haplotypes representing each species have been included in the reference datasets to allow —as far as possible— a comprehensive coverage of intra-specific variability.
  3. Blastn (algorithm: discontiguous MEGABLAST) will return a set of 30 reference sequences that represent the best hits with your sequence(s), summarized in a table including values of similarity (%) and coverage (%) between the query and the best hit sequences, and Expect values.
  4. You may visualize the phylogenetic position of your sequence(s)* within the selected set(s) of reference sequences, under a distance tree generated with the APE package using K2P distances and 500 bootstrap pseudo-replicates after aligning the sequences with Muscle.

*Note that clustering techniques are an alternative way of estimating the taxonomic affinities of your sequence(s) with proximate taxa, and should not be used for large-scale phylogenies.

Input files

Fasta sequence file
Fasta file which contains sequences to analyse
Use 12S gene file
Uncheck this if you don't want to blast on 12S gene
Use 16S gene file
Uncheck this if you don't want to blast on the 16S gene
Use COI gene file
Uncheck this if you don't want to blast on the COI gene
Use cytb gene file
Uncheck this if you don't want to blast on the cytb gene
Expect: upper bound on the expected frequency of chance occurrence of a set of HSPs (-e). The default value is 1e-10
The 'evalue' statistical significance threshold for reporting matches against database sequences; the default value is 1e-10
Type of model
Supported evolutionary model.
Select the name of a file or the actual data
if you are using Netscape 2.x or later, you can select a file by typing its name, or better, by selecting it with the Netscape file browser (Browse button)
OR you can type your data in the next area, or cut and paste it from another application.
(but not both)

Citation :
If you wish to cite DNAbushmeat, please use the following: Gaubert P., Njiokou F., Olayemi A., Pagani P., Dufour S., Danquah E., Nutsuakor M.E.K., Ngua G., Missoup A-D., Tedesco P., Dernat R., Antunes A. in press. Bushmeat genetics: setting up a reference framework for the DNA-typing of African forest bushmeat. Molecular Ecology Resources.

Based on Pise form generator version: 5.a (20 févr. 2014 15:50)