Questions tagged [makeblastdb]

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How to BLAST a protein against a large set of organisms?

I have a list of organisms with their full scientific names and Taxonomy IDs, total ~1500. I want to BLAST my protein against this 1500 genome or proteome. How can I do that? Here a sample protein ...
Supertech's user avatar
  • 596
0 votes
0 answers

IgBLAST Error: Germline annotation database could not be found in [internal_data] directory

I'm in the following situation and I came here to see if I could get some help. I'd like to use IgBLAST for an analysis on some Alpaca antibody data, so I received some FASTA sequences from a ...
Phantom Photon's user avatar
0 votes
1 answer

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 ...
K_081's user avatar
  • 105
1 vote
1 answer

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: ...
rimo's user avatar
  • 923
4 votes
1 answer

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 ...
Daniel Standage's user avatar
1 vote
1 answer

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 ...
accibio's user avatar
  • 145
1 vote
0 answers

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 ...
Luis ALberto's user avatar
1 vote
1 answer

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: ...
abraham's user avatar
  • 115
2 votes
1 answer

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: ...
MrTomRod's user avatar
  • 191
4 votes
2 answers

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 ...
juniper-'s user avatar
  • 890
2 votes
1 answer

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 ...
Bioathlete's user avatar
  • 2,574
2 votes
1 answer

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 ...
mRotten's user avatar
  • 192
2 votes
1 answer

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 ...
Hilda's user avatar
  • 21
3 votes
1 answer

The algorithm behind makeblastdb?

What is the algorithm/concept behind‚makeblastdb? I know makeblastdb produces a .phr, ...
Paul's user avatar
  • 317