Questions tagged [makeblastdb]

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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 ...
1
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1answer
26 views

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: ...
2
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1answer
1k views

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: ...
4
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2answers
759 views

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 ...
2
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1answer
299 views

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 ...
1
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1answer
218 views

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 ...
2
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1answer
341 views

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 ...
3
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1answer
386 views

The algorithm behind makeblastdb?

What is the algorithm/concept behind‚makeblastdb? I know makeblastdb produces a .phr, ...