1 reply to this topic

[Anusooya]

Hii, Iam working on stanalone blast version 2.2.23(win32) to run blastp. I am able to get text output. But i need Xml output for parsing with Biopython. The command line arguement i used was:

C:Program filesNCBIblast 2.2.23+bin -query final.fasta -db DBnr.06 -out result.txt

In some documentation I found -m7 or outfmt "7" will work. Its returns the text file itself starting with #Blast 2.2.23 instead of <?xml

Can anyone please help me with the command line to get output file in xml format as it is really urgent.

[Hamish McWilliam]

Firstly NCBI BLAST 2.2.23+ is rather old, I suggest you upgrade to the current 2.2.25+ release for a set of bug fixes and perfomance improvements.

From the '+' on the version number, you are using NCBI BLAST+ rather than the "legacy" NCBI BLAST. Unfortunalty the option values are slightly different between the two versions. So for "legacy" NCBI BLAST you would have used '-m 7' to get NCBI BLAST XML, for NCBI BLAST+ you need to use '-outfmt 5'. From the NCBI BLAST+ usage/help output obtained by running 'blastp -help':

 -outfmt <String>
   alignment view options:
	 0 = pairwise,
	 1 = query-anchored showing identities,
	 2 = query-anchored no identities,
	 3 = flat query-anchored, show identities,
	 4 = flat query-anchored, no identities,
	 5 = XML Blast output,
	 6 = tabular,
	 7 = tabular with comment lines,
	 8 = Text ASN.1,
	 9 = Binary ASN.1,
	10 = Comma-separated values,
	11 = BLAST archive format (ASN.1)

Which is a little different from that produced by "legacy" NCBI BLAST when running 'blastall -':

  -m  alignment view options:
0 = pairwise,
1 = query-anchored showing identities,
2 = query-anchored no identities,
3 = flat query-anchored, show identities,
4 = flat query-anchored, no identities,
5 = query-anchored no identities and blunt ends,
6 = flat query-anchored, no identities and blunt ends,
7 = XML Blast output,
8 = tabular,
9 tabular with comment lines
10 ASN, text
11 ASN, binary [Integer]