====== Bacillus thuringiensis serovar kurstaki BP865 (=KCTC 8689P) and serovar aizawai HD-133 ======
  * Title: Genome sequences of //Bacillus thuringiensis// serovar kurstaki strain BP865 and //B. thuringiensis// serovar aizawai strain [[http://nrrl.ncaur.usda.gov/cgi-bin/usda/prokaryote/report.html?nrrlcodes=HD-133|HD-133]]. [[https://doi.org/10.1128/genomeA.01544-16|Genome Announcements (2017) 5 e01544-16]].

===== ANI analysis (pyani) =====
{{ :anib_percentage_identity.png?480 |}}
{{ :anib_percentage_identity.pdf |}}

===== Placement of contigs into putative plasmids =====
Complete plasmid sequences for all //B. thuringiensis// strains were extracted from [[ftp://ftp.ncbi.nih.gov/refseq/release/plasmid/|RefSeq plasmid]] and were converted into blast database.

{{ :bt_plasmid.fna.gz |}}

Contig sequences were then searched against the custome DB using BLAST+ (blastn). Contigs with query coverages >= 95% were chosen for putative plasmidic sequences.

** Commands for blast search **

  blastn -query BP865_KRIBB.fna -db Bt_plasmid.fna -outfmt "6 std qcovs" -num_threads 30 -out out_BP865
  blastn -query BTaizawai_KRIBB.fna -db Bt_plasmid.fna -outfmt "6 std qcovs" -num_threads 30 -out out_BTaizawai
  
** Using different cutoff values **
^ BP865            |||||
^ Coverage (%)     ^ >=80  ^ >=85  ^ >=90 ^ >=95  |
^ No. contigs      | 94 | 85 | 92 | 87 |
^ Sum. contigs     | 935887 | 916779 | 916779 | 910387 |
^ Chromosome size  | 5472372 | 5491480 | 5491480 | 5497872 |

^ HD-133            |||||
^ Coverage (%)     ^ >=80  ^ >=85  ^ >=90 ^ >=95  |
^ No. contigs      | 93 | 90 | 87 | 77 |
^ Sum. contigs     | 920789 | 906873 | 848797 | 687161 |
^ Chromosome size  | 5517481 | 5531397 | 5589473 | 5751109 |

** Putative plasmid sequences **

{{ :bp865_plasmid.fna.gz |}} {{ :hd-133_plasmid.fna.gz |}}