two_bt_strains_2016
Table of Contents
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 HD-133. Genome Announcements (2017) 5 e01544-16.
ANI analysis (pyani)
Placement of contigs into putative plasmids
Complete plasmid sequences for all B. thuringiensis strains were extracted from RefSeq plasmid and were converted into blast database.
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
two_bt_strains_2016.txt · Last modified: 2021/03/17 13:09 by 127.0.0.1