Hi, i am new to bioinformatics analysis and currently researching whole genome sequence of Acinetobacter baumannii. I used SPAdes to perform assembly of genome and plasmidSPAdes to do the same for plasmid. After that, BLASTn against PLSDB database were performed on plasmid assembly using 95% identity and 90% qcov parameters. The results are already obtained with alignment length varies, however my question is :
- Is there any criteria (such as minimum alignment length) for determining plasmid from BLASTn output?
- For example, i obtained alignment length of 1068 from BLASTn result. After looking for the subject ID, the plasmid actually has 70kbp length. Is this valid to be reported as plasmid or should i neglect it?
- Also, i obtained several result for the same subject ID but in different start and end position. Same as question 2, is this valid to be reported as plasmid or should i neglect it?
Any help or suggestion will be appreciated.