Question: identify long stretches of DNA that 2 sequences share with low similarity (>85%)
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gravatar for Biomonika (Noolean)
4.0 years ago by
State College, PA, USA
Biomonika (Noolean)3.1k wrote:

I have two DNA sequences and I am interested in finding long stretches of DNA that these two sequences share. I prefer long stretches (up to 500 kb) with lower identity (> 85 %) rather than many shorter, perfect hits. Which programs and parameters would you recommend?

I started with blastn and tried to use as lenient parameters as I could, resulting in

blastn -db db.fasta -query query.fasta -outfmt 7 -gapopen 2 -gapextend 1 -penalty -1 -num_threads 30 -perc_identity 85 -word_size 20

but I still clearly see "breaks" in alignments, suggesting that the alignment extension is stopped before it hits new region with high identity. What else could I try? Still, I want my overall alignment to have at least 85 % identity.

Thanks

 

blastn • 1.3k views
ADD COMMENTlink modified 9 months ago by Biostar ♦♦ 20 • written 4.0 years ago by Biomonika (Noolean)3.1k

Have you tried Mauve?

ADD REPLYlink written 4.0 years ago by h.mon25k
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