create protein database for local Blast

Question

[BATMAN]

Hello friends, how're you? I wanted to know how I can do a blast against a database that I downloaded. I've downloaded a database of protein sequences from DEG (essential genes) and my idea is to do a blast against this database in my computer, using as input a long list of proteins.

The steps I performed so far were: 1) http://origin.tubic.org/deg/public/index.php/download (aminoacid sequence bacteria) 2) makeblastdb -in DEG-bacteria-db.faa -parse_seqids -dbtype prot

output:

   FASTA-Reader: Ignoring invalid residues at position(s): On line 91713: 44
    FASTA-Reader: Ignoring invalid residues at position(s): On line 102730: 48
    FASTA-Reader: Ignoring invalid residues at position(s): On line 110967: 18
    FASTA-Reader: Ignoring invalid residues at position(s): On line 112557: 18
    FASTA-Reader: Ignoring invalid residues at position(s): On line 112604: 18
    FASTA-Reader: Ignoring invalid residues at position(s): On line 112775: 18
    FASTA-Reader: Ignoring invalid residues at position(s): On line 113161: 18
    FASTA-Reader: Ignoring invalid residues at position(s): On line 113389: 18
    FASTA-Reader: Ignoring invalid residues at position(s): On line 113405: 18
    FASTA-Reader: Ignoring invalid residues at position(s): On line 113418: 18
    FASTA-Reader: Ignoring invalid residues at position(s): On line 113681: 18
    FASTA-Reader: Ignoring invalid residues at position(s): On line 113850: 18
    FASTA-Reader: Ignoring invalid residues at position(s): On line 114182: 18
    FASTA-Reader: Ignoring invalid residues at position(s): On line 114184: 18
    FASTA-Reader: Ignoring invalid residues at position(s): On line 114210: 18
    FASTA-Reader: Ignoring invalid residues at position(s): On line 114576: 18
    FASTA-Reader: Ignoring invalid residues at position(s): On line 114656: 18

I don't understand the warning, help

[lieven.sterck]

it means you have invalid characters where blast does not expect them.

Can you makes sure you downloaded a FASTA format file? and the unzipping went correctly?

[Andrzej Zielezinski]

Some of the sequences have invalid characters that are not amino acids. For example, there is a dollar sign at the end of the DEG10340547 sequence. But you don't have to worry about the warnings, BLAST ignores illegal characters.

Answer 1

[Mensur Dlakic]

I think the warnings should not be ignored, even if BLAST does so. For example, this error:

FASTA-Reader: Ignoring invalid residues at position(s): On line 114184: 18

translates into this sequence at that particular line:

>DEG10420110
Not available now.

There are many sequences with Not available now and I think they should be removed, because most of those letters are legitimate amino-acids even if spaces and periods are ignored. It may not be a bad idea to alert database authors that some of their sequences are corrupt.