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2 results for “multi-species dynamics”
Bacterial pathogens dynamic during multi-species infections
<p>Illumina gapA sequences of synthetic communities of plant bacterial pathogens: Pectobacterium and Dickeya genus. Sequencing was performed after growth on TSB synthetic medium (2 days post inoculation) or growth on potato tubers (5 days post infection).</p> <p> </p> <p>The following files are available:</p> <p>PT_table.txt: description of the potato tubers samples</p> <p>TSB_table.txt: description of samples in synthetic medium (TSB)</p> <p>gapA_PT.fasta.gz: Illumina fasta sequences after potato tubers infection (35,000 reads)</p> <p>gapA_TSB.fasta.gz: Illumina fasta sequences after synthetic medium inoculation (35,000 reads)</p> <p>gapA_without_primers.fasta: gapA sequences (without primers) of Pectobacterium and Dickeya strains used in this study (27 strains)</p> <p>species.txt: list of bacterial species used in this study (9 species)</p> <p>strains.txt: list of bacterial strains used in this study (27 strains)</p> <p>count.py: python3 script used to analyse the output of blastn</p> <p>R_script_FigureS1.R: R script for statistical analysis</p> <p>R_script_Figure2b.R: R script for statistical analysis</p> <p>R_script_Figure2a.R: R script for statistical analysis</p> <p> </p> <p>Method (examplified with the gapA_TSB sequences at the species level):</p> <p>• gapA sequences were blasted (blastn) against gapA sequences of Pectobacterium and Dickeya strains used in this study:</p> <p>makeblastdb -in gapA_without_primers.fasta -dbtype nucl -out dbblastn</p> <p>blastn -db dbblastn -query gapA_TSB.fasta -outfmt 6 -out blast.blastn -num_threads 12 -evalue 0.00001 -num_alignments 1</p> <p>• Reads count. Reads matching (100% identity) with gapA sequences of Pectobacterium and Dickeya strains used in this study were counted using the count.py python script. The output is a tab-separated values (.tsv) file:</p> <p>python3 count.py species.txt blast.blastn</p>
Data from: Dynamic multi-species occupancy models reveal individualistic habitat preferences in a high-altitude grassland bird community
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