ApicomplexanDB
<p> </p>
<p>Construction of Filarial Worm and Apicomplexan Haemoparasite Databases for NanoCLUST:</p>
<p>Within NCBI nucleotide the filarial worm COI gene Db was constructed using the search terms:</p>
<p>(((((((((((cytochrome c oxidase subunit 1[Title]) OR cytochrome c oxidase subunit I) OR cytochrome oxidase subunit 1) OR cytochrome oxidase subunit I) OR COX1) OR CO1) OR COI)) AND txid6295[Organism:exp])) AND 100:100000[Sequence Length])</p>
<p>And the NCBI accession NR_029255.1 (<em>Aliivibrio</em> <em>fischeri</em>) required for identification of our positive control. </p>
<p>Additionally a second filarial worm Db was constructed from the same sequences downloaded using the aforementioned search terms with the inclusion of the dog genome GCF_014441545.1 (<em>Canis lupus familiaris</em>). </p>
<p>For construction of the apicomplexan 18S rRNA gene Db the search terms used were:</p>
<p>((((((18S ribosomal RNA[Title]) OR 18S rRNA[Title]) OR ribosomal RNA[Title]) OR SSU rRNA[Title]) OR SSU ribosomal RNA[Title]) AND txid5794[Organism]) AND 200:10000[Sequence Length] </p>
<p>Plus the addition of NR_029255.1 (<em>Aliivibrio</em> <em>fischeri</em>) required for positive control identification. </p>
<p>The specific fasta sequences were chosen and downloaded as a fasta file from NCBI.</p>
<p>Extracted accession numbers from the fasta headers and produce a single column text file.</p>
<p>Downloaded the large NCBI accession2taxid database - a text file:</p>
<p>ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz</p>
<p>Created a mapping table of each accession to its taxa id using nucl_gb.accession2taxid</p>
<p>The awk command:</p>
<p>awk -F"\t" 'BEGIN{while(getline<"accession_ids.txt") hash[$1]=1} {if ($2 in hash) print $2,$3}' nucl_gb.accession2taxid > [Db_name]_map.txt</p>
<p>This will take a list of accession numbers "accession_ids.txt" and the downloaded accession2taxid database to produce a two column mapping file called [Db_name]_map.txt</p>
<p>Then used the makeblastdb command, downloadable from https://blast.ncbi.nlm.nih.gov/Blast.cgi</p>
<p>makeblastdb -in Filaria_AllCOI_species.fasta -parse_seqids -blastdb_version 5 -taxid_map [Db_name]_map.txt -title "[Db_name] database" -out [Db_name] -dbtype nucl</p>
<p>This produces the blast database, consisting of 10 files required by NanoCLUST. </p>
