BLAST에서 BLAST+로 명령어 바꾸기

BLAST에서 BLAST+로 명령어 바꾸기

BLAST	BLAST+	Specialty
megablast	blastn -task megablast	매우 비슷한 nucleotide sequence에 적용
bl2seq -i -j	blast -query -subject	하나의 sequence를 다른 것에 align
blastpgp	psiblast | deltablast	Position Specific Initiated BLAST
rpsblast -p F	rpstblastn	Translated Reverse Position Specific BLAST

BLAST/BLAST+ 인자 옵션

BLAST	BLAST+	Description
blastall	blastn, blastp, ...
-p	n/a	BLAST program: blastn, blastp, blastx, tblastn, ...
-i	-query	Input sequence file
-d	-db	BLAST database
-o	-out	Output file
-m	-outfmt	Output format: BLAST XML:7 TAB:8 | BLAST+ XML:5 TAB:6  *See more details below
-e	-evalue	Expectation value threshold
-a	-num_threads	Number of CPU cores to use
-F F	-dust no | -seg no	Disable low complexity filtering: DNA:dust AA:seg
formatdb	makeblastdb
-i	-in	Input sequence file
-p T/F	-dbtype prot/nucl	Molecule type
-o T	-parse_seqids	Parse and index sequence IDs
-n	-out	Base name for output files
fastacmd	blastdbcmd
-d	-db	BLAST database
-s	-entry	Search string
-D 1	-entry all	Dump database in FASTA format

Output Format 옵션

Options	BLAST (-m)	BLAST+ (-outfmt)
0	pairwise	pairwise
1	query-anchored showing identities	query-anchored showing identities
2	query-anchored no identities	query-anchored no identities
3	flat query-anchored, show identities	flat query-anchored, show identities
4	flat query-anchored, no identities	flat query-anchored, no identities
5	query-anchored no identities and blunt ends	XML Blast output
6	flat query-anchored, no identities and blunt ends	tabular
7	XML Blast output	tabular with comment lines
8	tabular	Text ASN.1
9	tabular with comment lines	Binary ASN.1
10	ASN, text	Comma-separated values
11	ASN, binary [Integer]	BLAST archive format (ASN.1)

Tabular format을 가장 많이 사용함으로 BLAST에서는 -m 8, BLAST+에서는 -outfmt 6 사용.

데이터에 따른 BLAST 사용

Query	Database	Comparison Space	Program to use
nuc	nuc	/nuc/	blastn
nuc	nuc	/Prot/	tblastx
Prot	Prot	/Prot/	blastp
Prot	nuc	/Prot/	tblastn
nuc	Prot	/Prot/	blastx

원본파일첨부

Quick_Start_Guide_BLAST_to_BLAST .pdf

Quick_Start_Guide_BLAST_to_BLAST .pdf

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