CFastaReader: Hyphens are invalid and will be ignored around line 288

Question

[baurumon]

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

Answer 1

[Brice Sarver]

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.