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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 conditionally required optional

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Input files

Fasta sequence file : please enter either :

1. Select a file:
2. or paste your fasta sequence here:
   

Use 12S gene file

Use 16S gene file

Use COI gene file

Use cytb gene file

1e- Expect: upper bound on the expected frequency of chance occurrence of a set of HSPs (-e). The default value is 1e-10

raw N TS TV JC69 K80 F81 K81 F84 BH87 T92 TN93 GG95 logdet paralin indel Type of model

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Some explanations about the options

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.

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)