Question: comparing two genomes
0
gravatar for dr_mm_sh
3.8 years ago by
dr_mm_sh0
Japan
dr_mm_sh0 wrote:

I am trying to find low similarity DNA sequences from two genomes of very closely related fungal species. Blast+ alignment of concatenated genomic sequences showed hits with identities around 70~80%. However, when I retrieved these DNA sequences of the both query and subject and made blastn search against genomes of each other, I was able to see hits with 100% identities.

What do you recommend to improve the accuracy of alignment results?

Command used to produce the alignment was:

$ blastn -db db_file -query input_file.txt -out output.txt -max_target_seqs 100 -outfmt 7

blast alignment • 1.2k views
ADD COMMENTlink modified 3.8 years ago by Sishuo Wang170 • written 3.8 years ago by dr_mm_sh0
0
gravatar for edrezen
3.8 years ago by
edrezen720
France
edrezen720 wrote:

Hello,

The blastn command actually executes the megablast algorithm by default. The megablast algorithm is very fast but finds fewer results than the blastn algorithm.

If you want to execute the blastn algorithm, you should try the following :

blastn -task blastn -db db_file -query input_file.txt -out output.txt -max_target_seqs 100 -outfmt 7

This post talks about this "-task" option.

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by edrezen720
0
gravatar for Sishuo Wang
3.8 years ago by
Sishuo Wang170
The University of British Columbia
Sishuo Wang170 wrote:

discontinuous megablast might also be helpful or you can change '-word_size' (=11 be default).

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Sishuo Wang170
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