I found cytoplasmic male sterility (CMS) occurs in a potato variety while never observed in another closely related variety. Now I already got the mitochondrial genome data (around 800K each) of these two varieties. How should I do the alignment to find the difference between them?
This can be done in two ways:
1. Predict genes in both genomes and compare the predicted gene/protein sequences
2. Assemble the reads of one genome on to another using Bowtie2 and identify the variations
Use the MEGA 7.0 version (molecular evolutonary genetic analysis) software for aligning the sequence. That is pairwise alignment using CLASTALW option.
Thank you
Although there are many alignment algorithms out there, CLUSTALW is one of the earliest and isn't as accurate as MUSCLE or MAFFT (see Nucleic Acids Research 32: 1792-1797; and Nucleic Acids Research 33: 511-518). Considering the length of the sequences that you want to align, MAFFT will produce the most accurate alignment (see Bioinformatics 34: 2490-2492). I use the web server to align whole chloroplast sequences (https://mafft.cbrc.jp/alignment/server/) because the computation power required for MAFFT or MUSCLE in stand-alone programs like MEGA7 or Geneious will crash your system unless you're using a super-computer.
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