Question: CFastaReader: Hyphens are invalid and will be ignored around line 288
gravatar for baurumon
7 days ago by
baurumon10 wrote:

enter image description here

Hi, I am doing reciprocal blast to find ortholog. for that i run i create database and run blastn and retrieve hit sequence fasta through awk 'BEGIN { OFS = "\n" } { print ">"$2, $3 }' blast.out > hit.fa but when i am trying to align hit.fa to reference genome database, i am getting this issue.

I used this command.--

blastn -query ~/Blast/hit.fa -db ~/Blast/omykiss/genome/omykiss -outfmt 6 -out blast_out -num_alignments 1

please help to solve it.

Thanks in advance

alignment • 70 views
ADD COMMENTlink modified 7 days ago by Brice Sarver2.8k • written 7 days ago by baurumon10
gravatar for Brice Sarver
7 days ago by
Brice Sarver2.8k
United States
Brice Sarver2.8k wrote:

Hyphens (coding for indels relative to another sequence, from BLAST in this case) are not in {A, C, G, T, N}. You should remove them or replace them with Ns, depending on what you're trying to do.

A quick Google search reveals this was an issue in some other applications, as well.

ADD COMMENTlink written 7 days ago by Brice Sarver2.8k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1404 users visited in the last hour