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| `Disrupted STOP codon` | The mutation changes a STOP codon to a different codon. | | ||
| `Premature STOP codon` | The mutation creates a STOP codon before the end of the annotated CDS. | | ||
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## Example Command Lines | ||
We provide example data from the *Drosophila melanogaster* SNPs used to test | ||
SNPMeta. These SNPs were constructed to have 60bp of sequence flanking each | ||
query SNP. To annotate the provided SNPs against the best match in GenBank, type | ||
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annotations will be written to `stdout`. Supply the `-o` argument to have to | ||
write to a file instead: | ||
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SNPMeta.py -f Example_SNPs.fasta -a '[email protected]' -l 60 \ | ||
SNPMeta.py -f Example_SNPs.fasta\ | ||
-a '[email protected]'\ | ||
-l 60\ | ||
-o SNPMeta_output.txt | ||
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To annotate the same SNPs against only *D. simulans*, it is possible to supply | ||
only the `-t` argument, but it gives better results to also supply the `-q` | ||
argument: | ||
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SNPMeta.py -f Example_SNPs.fasta -a '[email protected]' -l 60 \ | ||
-q 'Drosophila simulans' -t 'Drosophila simulans' | ||
SNPMeta.py -f Example_SNPs.fasta\ | ||
-a '[email protected]'\ | ||
-l 60\ | ||
-q 'Drosophila simulans'\ | ||
-t 'Drosophila simulans' | ||
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`-q` is applied to the results returned by BLAST (it sends an Entrez query to | ||
NCBI's servers), while `-t` acts on the GenBank records once they have been | ||
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