Entering edit mode
6.2 years ago
s.l.rinzema
•
0
Hi quick question!
I've done the same blast (tblastn) twice, the first one with the blast+ module and the second one with the standalone NCBI blast+ suite. Which uses the same blast module according to the cookbook. Though both give different results and as far as I can see the parameters are the same. Anybody know why? Am I missing something?
Thanks in advance!
If you mean standalone BLAST by
then you might want to check the version of local BLAST databases as using the different versions of the BLAST DBs would give you different output.
Thanks for the quick reply,
I forgot to mention I blast fasta against fasta. Not against a database.
You can make any fasta into a blast database with
makeblastdb
Thank you, but I don't think that's helpful and it doesn't explain why I get two different results.
Is it possible to provide an example of a query and the corresponding output e.g. in the BLAST tabular format that would help clarify what you mean by different results?
Hi I accidentally replied to you in another answer
Ofcourse! Here is my standalone BLAST commandline:
the python code i use to from biopython:
I now see that my BioPython code's output is in XML format and my commandline is in pairwise (the standard). If i add the "-outfmt 5" to the commandline I get the same result as my BioPython code but it's different as with the pairwise. Now my question is why? Still thank you! I guess this solved my problem and brought me to another
Maybe top BLAST hits were not in the same order? You could get output in the tabular BLAST format using
-outfmt 6
option and parse the hits for each query and check if it is just the order that was different or there were discrepancies in the corresponding evalue and bitscore.Thank you for your help, I already fixed it by changing the output to XML. With both outputs as XML the evalues and hits were exactly the same!