I have 1 plasmid sample sequenced on MiSeq PE150. I have derived the sequence of putative plasmid by de novo assembly (SPADes). The plasmid contains 5' AOX1 primer sequence and reverse complement of 3' AOX1 primer along with possible insert sequence.
I have 2 genomic DNA sequenced on MiSeq PE150. I wish to find partial sequence of the AOX1 gene with vector DNA inserted from these two samples.
I have the 5' AOX1 and 3' AOX1 sequences.
How can I achieve this? Can someone suggest any strategy?