How to identify mutations from FASTA sequences?

Question

[Anisur Rahman]

I have two full genome sequences (in Fasta format) plus annotation file (in gff format) from same organism. One sequence is the reference genome and another is my test sequence.

Would you please suggest me some pipeline or tools ( preferably, R or bash based tool) by which I will be able to generate following results by comparing test seq against reference seq:

• List of mutations in nucleotide and protein level along with their positions.
• List of SNPs and their positions
• List of indels and their positions

I will apply same pipeline for many other test sequences in Fasta format.

NB: I don't have short reads (in Fastq format with quality) for these sequences. So I have to perform the anaysis by plain Fasta files.

Thanks in advance.

[Ankit]

Create index for reference genome and align your test genome fasta to that reference.

You can also split your test fasta into multiple files if your test genome is too large and then align to reference genome.

After alignment you can call variants against the reference genome.

[Wakala]

Do you mean RNA editing?