1.

-dbtype <String, nucl',prot'>
Molecule type of target db
-parse_seqids
Option to parse seqid for FASTA input if set, for all other input types
seqids are parsed automatically

2.

# Build the blast index.
makeblastdb -in index/all-proteins.fa -dbtype prot -out index/all -parse_seqids

# Run the blast queries.
blastp -db index/all -query L.fa

# Customize the output even more.
blastp -db index/all -query L.fa -outfmt "7 qseqid sseqid pident"

# Three best alignments
blastp -db index/all -query L.fa -outfmt "6 qseqid sseqid pident" | sort -k3 -rn | head -5

# The worst alignments.
blastp -db index/all -query L.fa -outfmt "6 qseqid sseqid pident" | sort -k3 -rn | tail -5

outfmt 6为m8格式。

3.

fasta之外是makedb的输出。

db