Questions tagged [makeblastdb]
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Blast output file only shows 500 lines -outfmt 6
I had created databases of different sets of metagenome datasets - one with 6 runs, other with 48 runs, another with 100 runs, etc using the accession list for each of these datasets and makeblastdb ...
Fixing FASTA file for Local BLAST Database
I recently prefetched 157 SRA files from an NCBI BioProject using the SRAtoolkit. I then used the toolkit to download those files in FASTA format. Each individual FASTA file looks something like this: ...
Assign multiple taxids to a sequence when constructing a local BLAST database
I recently had a script fail due to poor handling of BLAST output. The BLAST -outfmt staxids field usually returns a single taxid, but occasionally it returns two ...
makeblastdb creating multiple files of unexpectedly large sizes
I have a set of 100 amino acid sequences and I want to perform a BLASTP sesrch against the refseq_protein database. Accordingly I had set up the standalone version ...
Blastn locally nt database search length < 16
when I run a short search in blastn locally with less than 16 nucleotides with nt.00 database I don't get any found match, but if I increase the searched string 2 nucleotides it finds matches, so the ...
blastp option to compare with a personal database
I'm trying to compare proteins generated with prokka (from a genome) with blastp using a virulence factor database VFDB, and I want to use some parameters obtained from this paper: ...
Cannot blast database created with blastdb_aliastool: BLAST Database error: No alias or index file found
I want to merge/concatenate BLAST databases as suggested here. This is my example script that explains what I'm trying to achieve better than words can: ...
How is BLAST's nr database created?
Is there a paper or web page describing the procedure for creating the nr database used by NCBI's BLAST implementation? I presume it's some type of clustering, but I'm curious about how exactly ...
Merging / Concatentating BLAST Databases
I was wondering if any one has had success merging BLAST databases from multiple references? For a concrete example I have hg19 and a bunch of viral and bacterial genomes that all have been index ...
Hits in Primer-BLAST not found with programmatic blastn query
Summary: I'm writing an automated tool for designing Sanger sequencing primers (other tools don't do exactly what I want) that will be incorporated in a production diagnostic laboratory for on-demand ...
Error in PSI-BLAST when running psipred locally
I am very new to bioinformatics and Linux and am trying to run psipred locally on Ubuntu 18.04 but cannot get PSI-BLAST to work. I have downloaded BLAST legacy version 2.2.26 and unpacked it, uniref90 ...
The algorithm behind makeblastdb?
What is the algorithm/concept behind‚makeblastdb? I know makeblastdb produces a .phr, ...