I am trying to make phylogenetic trees of ABC transporter protein sequences(actually translated contigs - transcriptome data) of Coleus with ABC transporter protein sequences of Arabidopsis thaliana. For some protein sequences of coleus i got different results in different frames of protein in BLASTP, probably it is due to a stop codon but i have no clear idea, how to solve the problem of stop codon. How to get the full protein sequence for aligning it with Arabidopsis ABC Protein sequences ?
You can use Arabidopsis ABC transporter protein sequence to do the BLASTP and you will find the sequence in Coleus genome. If you want to clone the sequence, you can design the primers use Arabidopsis ABC gene sequence, and Coleus DNA as template, after you got the bands, just sequencing the bands, and then do the BLASTP.
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