Question: BLASTn output format start position larger than stop position
gravatar for nataliagru1
4 months ago by
nataliagru150 wrote:

Dear Community,

I am currently running an experiment to identify gene expansion in parasite genomes. I have collected respected gene sequences and created a blast database of my parasite reference genomes using blast db function.

I use blastn and search against my parasite reference genome with my collected gene sequences as query using the command:

blastn -query HSP_collectedseqs.fa -db parasite_database -outfmt 6 -out experiment1.blast -task blastn -evalue 0.0001

I noticed in my output fmt 6 blast file that some of the hits have start positions that are larger than their end positions. For example:

human-HSP8 pathogen_contig_019288 73.71 175 46 0 1076 1250 7 181 6e-22 109

So you can see that for subject start and subject end respectively its 7 and 181.

How is this possible? Is there an error in my code? I have searched through the documentation/manual and turned to the internet but cannot find a definitive answer as to what this could mean.

Any guidance is greatly appreciated!

ADD COMMENTlink modified 4 months ago by Sej Modha4.7k • written 4 months ago by nataliagru150

Nothing to worry about.

 9.      sstart      start of alignment in subject
10.      send    end of alignment in subject

See: A: s. start and s.end in tabular BLAST output are the wrong way around?

ADD REPLYlink modified 4 months ago • written 4 months ago by genomax89k
gravatar for Sej Modha
4 months ago by
Sej Modha4.7k
Glasgow, UK
Sej Modha4.7k wrote:

Default BLAST settings will perform searches in both strands. As shown in blastn -help

 -strand <String, `both', `minus', `plus'>
   Query strand(s) to search against database/subject
   Default = `both'
ADD COMMENTlink written 4 months ago by Sej Modha4.7k

Thank you very much for your response. It seems as though I didn't intuitively read the manual. Its clear to me now! Greatly appreciated

ADD REPLYlink written 4 months ago by nataliagru150
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