Create a costum taxonomy file
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4.0 years ago

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 • 849 views
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This has been discussed in a previous question without a satisfactory conclusion : C: Insert sequence in nt database

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

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4.0 years ago
GenoMax 142k

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
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