5

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 column, qlen, and the 13th columns, slen, and get the percentage higher than 50. awk -F'\t' '{ if ($NF >= 50) printf "%s\t%.2f\n", $0 , ($2/$5)*100 }' result.txt Check the documentation for the ...


4

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 is (I think) defined very strictly as proteins that are identical in terms of sequence and length, so the clustering is trivial, without the need for a ...


4

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 the normal runpsipred script.


2

The problem was that the database must be specified without suffix, i.e. blastn -db testdb as opposed to blastn -db testdb.nal. By the way, it produces exactly the same output as blastn -db "FAM1079.ffn FAM3228.ffn FAM6161.ffn FAM19036.ffn" -query query_single_nucl.fasta -outfmt 6 and the performance is not better.


2

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 6. Non-redundant defline syntax The non-redundant databases are nr, nt and pataa. Identical sequences are merged into one entry in these databases. To be merged two sequences must have identical lengths and every residue at every ...


2

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 C++ toolkit as the command makembindex so I'm inclined to think the current implementation must have been derived from this strategy. Looking at the relevant ...


1

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 can provide multiple database names to the “-db” parameter, or to provide a GI file specifying the desired subset to the “-gilist” parameter. However for these ...


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