I am working on genome & chromosomal properties of Bambara groundnut. My interest is in centromeric DNA -tandem repeats.
I used primers from cowpea which is a closely related specie to bambara. After cloning & blasting the sequences,I could not get the gene of interest though got a vigna specie. Moreso, multiple alignment of the clones showed less identity.
(1). What could be the problem?
(2).Also, I am having challenges interpreting my sequence analysis results since there are lacking materials available with regards to the specie of study. Any help will be well appreciated. Recommendations are also welcomed.
Thanks in anticipation.
No need to do alignment because as you said you could not get good clones. That means your primers are not working good. You might need to design new specific primers. After that do cloning and make sure that you are choosing the correct colonies, with the insert.
You first step in cloning seems to be wrong in this experiment. Thus, interpretation of wrong data would not make much sense.
Dear Abhijeet singh,
Thanks for the contribution. Mean a lot to me.
With regards to the cloning, I first run a PCR using the specific primers from cowpea. 1kb of PCR fragment was cloned,miniprep and sent for sequencing. I analysed the sequence results before blasting in ncbi.
Was there anything I missed please?
Thank you
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