5 votes
Accepted

blastp option to compare with a personal database

You can use these options: blastp -query my.faa -db VFDB.fas \ -perc_identity 50 -outfmt 6 \ -evalue 10e-5 -out results.txt Then select the 5th ...
zorbax's user avatar
  • 769
4 votes

How is BLAST's nr database created?

The Refseq team and also the NCBI resource coordinators team publish a new paper every few years, so check out the many papers (e.g. here or here), but to answer your 2nd question, non-redundancy here ...
Chris_Rands's user avatar
  • 3,948
4 votes

Error in PSI-BLAST when running psipred locally

This error could be due to the fact that you are using legacy blast, have you tried using BLAST+ instead? If you wish to use PSIPRED with BLAST+, then use the runpsipredplus script here, rather than ...
Pawan Verma's user avatar
4 votes
Accepted

Assign multiple taxids to a sequence when constructing a local BLAST database

I inquired with the NCBI BLAST help desk today, and within an hour they provided a very helpful response. To summarize, when redundant records in the database are collapsed, the deflines (accessions + ...
Daniel Standage's user avatar
2 votes
Accepted

makeblastdb creating multiple files of unexpectedly large sizes

Welcome to the Bioinformatics site! Hopefully you find the below helpful. Regarding the creation of a RefSeq protein database locally...as you mentioned, there are pre-made RefSeq BLAST databases ...
Scot's user avatar
  • 782
2 votes

Cannot blast database created with blastdb_aliastool: BLAST Database error: No alias or index file found

The problem was that the database must be specified without suffix, i.e. blastn -db testdb as opposed to blastn -db testdb.nal. ...
MrTomRod's user avatar
  • 191
2 votes
Accepted

How is BLAST's nr database created?

Did a little more searching and found the answer in the README on BLAST's ftp site: ftp://ftp.ncbi.nlm.nih.gov/blast/db/README ...
juniper-'s user avatar
  • 900
2 votes
Accepted

The algorithm behind makeblastdb?

From looking at this publication "Database indexing for production MegaBLAST searches" which although deals with MegaBLAST and it's indexing method, it would appear that this was rolled into the NCBI ...
Matt Bashton's user avatar
  • 1,069
2 votes
Accepted

Merging / Concatentating BLAST Databases

There's an app for that, apparently. Often we need to search multiple databases together or wish to search a specific subset of sequences within an existing database. At the BLAST search level, we ...
terdon's user avatar
  • 10.1k
2 votes

Fixing FASTA file for Local BLAST Database

Briefly the best strategy I think is to download fastQ files and process this via an assembler. I wouldn't enter raw short read Illumina data into a local Blast database. What I'm pretty certain of is ...
M__'s user avatar
  • 12.3k
1 vote
Accepted

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

My solution is simply. perform a web-based Blastp using the following parameters: most dissimilar 5000 hits (maximum limit) Restrict to Archaea (which is what you samples appear to be)* If you hit ...
M__'s user avatar
  • 12.3k
1 vote

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

In the interface of blastp, you can limit the search space to organisms you want to. Yo can do this by introducing name species or Tax IDs, you can add more than one, but I bet you don't wanna ...
JRodrigoF's user avatar
  • 827
1 vote
Accepted

Blast output file only shows 500 lines -outfmt 6

I've reproduced the issue. The solution is to simply set -max_target_seqs to whatever number of hits you want. E.g. ...
M__'s user avatar
  • 12.3k
1 vote
Accepted

Hits in Primer-BLAST not found with programmatic blastn query

I've found the problem, and it's way less interesting than I initially thought. Essentially, my "eValue" was way too low. Instead of -evalue 100, I'm now using <...
mRotten's user avatar
  • 192

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