What input does blastdb_aliastool need?

Question

[ronaldnieuwenhuis]

Hello, I want to use the blatdb_aliastool to aggregate multiple databases. But I am wondering if the -dblist option uses .FASTA files or .nsq files? If tool can only be used with .nsq files it means I have to use makeblastdb for all my fastafiles I guess?

Answer 1

[pld]

I believe that if your goal is to generate multiple databases from one, you simply specify a list of precompiled blast databases using the -dblist option.

This means that the input is precompiled blast databases, not fasta files. If these databases are not already compiled, you will have to compile them with makeblastdb.

[ronaldnieuwenhuis]

May I ask you for a little clarification of your answer. Do you mean with precompiled blast databases a directory consisting of multiple .nsq, .nin, .nhr files? Maybe you can provide me an example of how the -dblist argument has to look like?

[pld]

As it says in the documentation for blastdb_aliastool, the option -dblist requires a list of database names, not specific files.

In general, when any of the blast programs ask for a database, they only want the database name. Typically a blast database is created with several files with the same name but different extensions, blast programs only need to know the name of the file, each program knows which files it needs so one does not have to provide any extensions.

e.g. If I had a database called myblastdb, there would be several files myblastdb.nsq, myblastdb.nin, myblastdb.nhr, but I only need to specify the name, myblastdb, to a blast program.

[ronaldnieuwenhuis]

Thank you for your time and answer sir, it worked out for me! :) The databases I created with makeblastdb were not giving an -out argument so all my databases were called <dbname>.fa.nsq and so on. So I confused meself, but the problem is solved.

Answer 2

[rtliu]

Aggregate existing BLAST databases

To combine the two nematode nucleotide databases, named “nematode_mrna” and “nematode_genomic", we use the following command line:

$ blastdb_aliastool -dblist "nematode_mrna nematode_genomic" -dbtype nucl -out nematode_all -title "Nematode RefSeq mRNA + Genomic" 

The above example is copied from BLAST Command Line Applications User Manual

[Sophia Sue]

hello，i use my datas to test this command, aiming to merge the two reference genome files into one file: $blastdb_aliastool -dbtype nucl -dblist "GCA_000008525.1_ASM852v1_genomic.fna GCA_000011725.1_ASM1172v1_genomic.fna" -out hp_ref_genome_577.fna -title "AE000511.1 AE001439.1" but there is sometiong wrong : "BLAST Database error: BLASTDB alias file creation failed. Some referenced files may be missing", maybe this is due to the parameter "-title", could you tell me the "-title" usage more clearly or figure out the error above. thanks a lot!