BLAST output

Question

[torquato.f.o]

Hi all,

I am running blast+/v2.8.1 as follow:

blastn -db mydatabase_db -query mysample.fa -out resultsblast -evalue 1e-6 -perc_identity 90 -max_target_seqs 10 -num_threads 8 -outfmt 7

See the output below.

How can I see a list of true hits found?

# BLASTN 2.8.1+ 
# Query:  
# Database: mydatabase_db
# 0 hits found
# BLASTN 2.8.1+
# Query: CLocus_20_Sample_32_Locus_20_Allele_0 [QSI_A1]
# Database: mydatabase_db
# 0 hits found
# BLASTN 2.8.1+
# Query: CLocus_20_Sample_32_Locus_20_Allele_1 [QSI_A1]
# Database: mydatabase_db
# 0 hits found
# BLASTN 2.8.1+
# Query: CLocus_20_Sample_33_Locus_20_Allele_0 [QSI_A2]
# Database: mydatabase_db
# 0 hits found
# BLASTN 2.8.1+
# Query: CLocus_20_Sample_33_Locus_20_Allele_1 [QSI_A2]
# Database: mydatabase_db
# 0 hits found
# BLASTN 2.8.1+
# Query: CLocus_20_Sample_34_Locus_20_Allele_0 [QSI_A3]
# Database: mydatabase_db
# 0 hits found
# BLASTN 2.8.1+

[GenoMax]

I guess you are using -outfmt 7 to see queries that don't have hits because otherwise you can simply use -outfmt 6 to only get results for queries that have hits.

Answer 1

[Mensur Dlakic]

This can mean a couple of things. The most obvious one is that there are no matches for your sequences in the database, which is what the program is telling you. It can mean that you have a protein database but your query is nucleic, in which case you need to use blastx. If your query sequences are short, you may need to use the option -task blastn-short. Finally, you may need to lower the percent identity option.

[torquato.f.o]

Many thanks Mensur, I thought about both of your hypotheses just before sleeping.

[GenoMax]

Did one of those hypotheses apply in your case? You just showed us a snippet of results that do not have any hits but there may be other queries further below which may actually have results and then my comment will apply.