I am using bl2seq(2.2.25) to blastn two fasta files. I am not sure I fully understand how the (-e) parameter works.
I thought the -e parameter was a cut off e-value and would therefore show all results with a e_value under 10 given my current parameters.This is not what I am seeing. Can someone please explain why?
EXAMPLE:
When I set my e_value to 10 (-e 10) I am missing some results that have an -e value under 10. I know this because when i set it to -e 50 (using the same parameters) I get more results of e values under 10.
NOTICE: the 0.09 e values have one more when i set my e value to 50
/blast-2.2.25/bin/bl2seq -p blastn -D 1 -E 2 -q -2 -r 1 -G 5 -W 7 -F T -e 10.11 -i '1.fasta' -j '3.fasta' -I 35606641,35636750 -J 66649067,6668249735606641,35636750 -J 66649067,66682497
BLASTN 2.2.25 [Feb-01-2011]
Query:
Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
QUERY 88.89 72 5 1 35624525 35624593 66670273 66670344 8e-17 83.4
QUERY 79.37 63 13 0 35625030 35625092 66670905 66670967 8e-06 46.8
QUERY 79.66 59 12 0 35618518 35618576 66660799 66660857 3e-05 44.9
QUERY 82.81 64 9 2 35624843 35624905 66670679 66670741 4e-04 41.1
QUERY 95.45 22 1 0 35618611 35618632 66660909 66660930 0.006 37.2
QUERY ...