create protein database for local Blast

create protein database for local Blast

1

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) 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


makeblastdb

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