Question: (Closed) Command Line blast not returning the same results as web blast
gravatar for Jacob
21 months ago by
Jacob10 wrote:

Right now I'm trying a general blast for everything and then searching for the matches by taxid or the seqid's. I'm tried other approaches using gilists and downloading genomes and have still not obtained the results I need.

These are the results I receive from the online version when I search for Arsb transcript variant 1, for organism Gallus gallus (taxid: 9031), an e value cut off of 0.00005, on database refseq_genomic

Database: NCBI Genomic Reference Sequences
           23,370,420 sequences; 1,019,245,483,979 total letters
Query= NM_005445.3 Homo sapiens structural maintenance of chromosomes 3
(SMC3), mRNA


                                                                                             Score     E
Sequences producing significant alignments:                       (Bits)  Value

NC_006093.4  Gallus gallus isolate RJF #256 breed Red Jungle f...  237     3e-59
NT_455898.1  Gallus gallus isolate RJF #256 breed Red Jungle f...  237     3e-59

I am running a command line blast query which to my understanding should have the two lines of results within the output file. These lines are not in the output however

    blastn -query mRNAfiles/Arsb -db database/refseq_genomic -out "blast_output.txt" -evalue 0.00001 -outfmt '6 qseqid sseqid pident evalue bitscore score qcovs qcovhsp qcovus staxids ssciname'. //This command should show all results for all organisms

When I grep for the organisms taxid and the refseq ids of the output, I do not find anything

grep '9031' blast_ouput.txt  
grep 'NC_006093.4' blast_output.txt 
grep 'NT_455898.1' blast_output.txt
blast+ blastn blast • 1.1k views
ADD COMMENTlink modified 20 months ago by Biostar ♦♦ 20 • written 21 months ago by Jacob10

Please search biostars (use google for an external search) next time : Why the local blast and online blast produce different results?
Blast searches are sensitive to the type and size (content) of the database beings searched against along with settings for gap opening/extension penalty. You will have to check all of those things.

ADD REPLYlink modified 21 months ago • written 21 months ago by genomax62k

I feel like I have been, I guess I haven't?

ADD REPLYlink written 21 months ago by Jacob10

No problem, sometimes it is hard to find. But this question comes up once in a while.

ADD REPLYlink written 20 months ago by Michael Dondrup45k

Hello Jacob!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.


ADD REPLYlink written 20 months ago by Michael Dondrup45k
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