This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Create a costum taxonomy file

I want to merge some sequences created from my lab with the nt databases. So I did a makeblastdb command and then blastdb_aliastool.However the blast output doesn't give me a taxonomic name, it returns NA. So now, I want to create a costume taxonomy file. Here is an example of my fasta headers:

>se1 name_species gene

>se2 name_species gene

And then I created the custom taxonomy file like this:

se1 123452
se2 123445

I added the -taxid_map to the makeblastdb command, but results continues to be NA... Thanks for the help

blast
• 1,329 views • link
updated by GenoMax GenoMax • written by anasofiamoreira94 anasofiamoreira94

i created a new post because the other is extensive... I did the suggested editing but I continue to have NA

• 0 views • link
written by anasofiamoreira94 anasofiamoreira94

1 answer

This is working for me with blast+ 2.10.0. I did not test this with an aliased database but I expect that should work as well.

$ more test_map.txt 
test1 345
test2 23
test3 5678
test4 4

$ grep ">" db_dna.fa 
>test1
>test2
>test3
>test4

$ makeblastdb -in db_dna.fa -dbtype nucl -title "some sequences I found" -out mysequences -parse_seqids -taxid_map test_map.txt 

$ blastn -task blastn -query my.fa -db mysequences -out dhhf.out  -outfmt '6 qseqid sseqid evalue bitscore sacc staxid'

$ more dhhf.out 
test_seq        test1   0.0     2147    test1   345
test_seq        test1   0.010   30.1    test1   345
test_seq        test1   0.010   30.1    test1   345
test_seq        test1   1.4     22.9    test1   345
test_seq        test1   1.4     22.9    test1   345
test_seq        test4   0.12    26.5    test4   4
test_seq        test4   1.4     22.9    test4   4
test_seq        test4   5.1     21.1    test4   4
test_seq        test4   5.1     21.1    test4   4
test_seq        test2   5.1     22.0    test2   23
test_seq        test2   5.1     21.1    test2   23
• 0 views • link
written by GenoMax GenoMax

Log in to answer this question.

More posts like this