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 ...
- 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 ...
- 3,928
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 ...
- 63
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 + ...
- 5,060
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 ...
- 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.
...
- 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
...
- 890
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 ...
- 1,059
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 ...
- 9,452
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__♦
- 11.3k
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__♦
- 11.3k
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 <...
- 192
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