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--- two_bt_strains_2016 [2016/11/15 17:51] – [Placement of contigs into putative plasmids] hyjeong
+++ two_bt_strains_2016 [2021/03/17 13:09] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
 ====== 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]]
+  * 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) =====
@@ Line 11: / Line 11: @@
 {{ :bt_plasmid.fna.gz |}}
-Contig sequences were then searched against the custome DB using BLAST+ (blastn)
+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 |}}