blastn does not blast everything?

Question

[hpatzenhauerova]

Hi all, is it normal that blastn does not blast all query sequences? I used blastn and the input file has 860 sequences, but in the output file there are only 400 blasted

Thank you

[GenoMax]

Your post lacks sufficient detail to provide a complete answer. You should add information about following questions to the original post.

Where did you do this search? Locally or on web at NCBI? Were there any error messages produced? What format was the output in (tabular)? Have you checked to see if the remaining 460 showed "no hits"?

[hpatzenhauerova]

You are right, sorry for that. IIt is solved, it was a problem with output format.

Thank you for your answer :)

Answer 1

[lieven.sterck]

No it that is in theory not normal. Your blast finished OK, we can assume, so not out-of-memory or walltime issues?

However, how do you decide it did not BLAST every query? it can of course very well be that you can't find it in the output because it did not has any hits. If you are using -outfmt 6 (so tabular) format it will indeed not be present in the output. For all other outformats you should see a note indicating it has no hits (No Hits Found)

[hpatzenhauerova]

Thank you very much, I thought that the missing ones are those with 0 hits, but was not sure how to show it. I used -outfmt 6 and did not know that the other options shows also no hit results. Thanks and have a nice day :)

Answer 2

[Buffo]

There are lot of reasons to not blast anything, It is normal when there are no similitudes to your database.

Answer 3

[Joe]

Check the default cutoffs (or your own parameters). If there were no hits for some of your sequences that matched the thresholds for E-value, they wouldn't be included in the output.

But as others said, we need far more information about how you ran it to answer this properly.