After assembly , sometimes for each locus we get more than one transcript ( I thinks because of 1. alternative splicing or 2.several gene from same family that share same domain 3. sequencing from different part of genes but did not overlap to match other fragment, Am I right? ).
and that s why when I did blast against one specific gene I got several hits. So now , how can I choose the best hit of one gene ? I mean which transcript of one locus is the best for further study like templat for design primer?
Thank you in advance