Suppose there are sequences for Protein A and B.
Nucleotide sequences of A and B have a 73% identity and 73% similarity.
Amino acid sequences of A and B have 98% identity and 99% similarity.
Can they be called alleles?
How alleles can be identified from sequence alignment?
Hello, Hasan san,
For your question, there can be other simple ways that can give you the answer. This question must be related to BLAST. But I like to suggest a way that I learned and used in identifying the genomic regions. I hope this will help you as well.
I first find a suitable reference genome with the annotation file and create other files including index files. Then align my sample genomes against the reference genome. If there are many files I will merge all the files to create one file. As the next step, I call the variants and create a vcf file. Finally, I upload the reference, annotation, and vcf files to IGV software and observe the genic regions.
In the process, I use BWA, Samtools, and Picard, GATK, or deep variant, glnexus.
With my studies, I learned some of the above programs but some I just started using. Open for further corrections of the answer.
Hello Ginushika Premarathne San,
Thank you very much for your answer. I will try your method.
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