Changing evalue doesn't change the results of blast

Question

[arronar]

Hi!

First's run results occurred by this command:

tblastn -query query.fasta -db plant_DB -out output-evalue -html

and in some reads I got two targets. e.g :

Score =   160 bits (404),  Expect = 1e-44, Method: Composition-based stats.
 Identities = 76/77 (99%), Positives = 77/77 (100%), Gaps = 0/77 (0%)
 Frame = +3

Query  1016  GLPGVNGLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDARAAAIVMRTVRNTVDTGRTV  1075
             GLPGV+GLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDARAAAIVMRTVRNTVDTGRTV
Sbjct  3     GLPGVDGLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDARAAAIVMRTVRNTVDTGRTV  182

Query  1076  VCTIHQPSIDIFEAFDE  1092
             VCTIHQPSIDIFEAFDE
Sbjct  183   VCTIHQPSIDIFEAFDE  233


 Score = 50.4 bits (119),  Expect = 2e-06, Method: Composition-based stats.
 Identities = 25/74 (34%), Positives = 45/74 (61%), Gaps = 1/74 (1%)
 Frame = +3

Query  346  VRGISGGQRKRVTTGEMLVGPANALFMDEISTGLDSSTTFQIVKSLRQAIHILGGTAVIS  405
            V G+S  QRKR+T    LV   + +FMDE ++GLD+     +++++R  +   G T V +
Sbjct  15   VDGLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDARAAAIVMRTVRNTVDT-GRTVVCT  191

Query  406  LLQPAPETYDLFDD  419
            + QP+ + ++ FD+
Sbjct  192  IHQPSIDIFEAFDE  233

I want to get back only the first target and that's why i changed the -evalue parameter into this:

tblastn -query query.fasta -db plant_DB -out output-evalue -html -evalue 3.1

but the results are still the same.

Any idea to filter them better?

Thank you.

[Devon Ryan]

Both E values in those hits are well below 3.1, so why would you expect them to be filtered?

[arronar]

Oh sorry! The second command is wrong.

That's the right one.

tblastn -query contig2-query.fasta -db HorseWeed_Transcriptome_DB -out output-evalue -html -evalue 1.0

I don't want the second one to be appeared.

[Devon Ryan]

Then you'd need to use a threshold of <2e-6.

Answer 1

[hpmcwill]

The E-value threshold in BLAST is an upper limit, so a threshold of '3.1' is greater than the E-value reported for the hits (1e-44 and 2e-06), and thus they are reported. The use of scientific notation for the E-value, can be a bit confusing since the exponent has a large magnitude for very small numbers. In this case we have:

• 1e-44 = 1 * 10^-44 which is less than 3.1 * 10^0
• 2e-06 = 2 * 10^-6 which is less than 3.1 * 10^0, or in normal decimal notation: 0.000002 < 3.1

As noted by Devon, in order to exclude the second hit by E-value, you would need to use a value between 1e-44 and 2e-06, say 1e-07.