This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Taxonomy from blast file

Hello everyone!

I only have tsv file with the result of the BLAST algorithm (out format 6). How to understand the organism, for example viruses, which nucleic acids were found in the sample?

Line example of the file:

97206   LN899827.1      89.333  75      5       3       37      109     5520034 5519961 1.87e-14        91.6

Thanks!

blast taxonomy
• 1,703 views • link
updated by SequenceServer • SequenceServer • written by Anst • Anst

1 answer

Depending on how big the BLAST search was, you could do one of the two things.

  1. Re-run BLAST analysis with taxonomy formatted databases and include customised fields in the tabular output e.g.sscinames, staxids etc (https://www.ncbi.nlm.nih.gov/books/NBK279684/table/appendices.T.options_common_to_all_blast/)
  2. Another option would be to use NCBI eutils to fetch taxonomy from accession numbers (e.g. Convert list of Accession Numbers to Full Taxonomy and https://github.com/jrjhealey/PYlogeny)
• 0 views • link
written by Sej Modha Sej Modha

@Sej Modha's replies are perfect..

But it's obviously annoying to have to rerun things! So I just wanted to briefly note that SequenceServer allows you to download the other outputs (including the extended tabular output which includes all possible columns without rerunning any analysis).

• 0 views • link
written by SequenceServer • SequenceServer

Log in to answer this question.

More posts like this