Entering edit mode
11.4 years ago
agatorano
▴
50
I was wondering if there was full explanation for each of the pieces of this part of the output.
Lambda K H
0.328 0.141 0.440
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 455
Number of Sequences: 0
Number of extensions: 40
Number of successful extensions: 2
Number of sequences better than 100000.0: 1
Number of HSP's better than 100000.0 without gapping: 1
I am confused by this part of the output and was wondering if there was a full explanation anywhere.
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 1
length of query: 221
length of database: 456,953,620
effective HSP length: 122
effective length of query: 99
effective length of database: 456,953,498
effective search space: 45238396302
effective search space used: 45238396302
T: 9
A: 40
X1: 15 ( 7.1 bits)
X2: 129 (49.7 bits)
X3: 129 (49.7 bits)
S1: 37 (20.3 bits)
S2: 37 (18.9 bits)
I have a lot of educated guesses for most of them but I don't know if I understand the innards of BLAST well enough to be completely sure about any of my assumptions.
I am just curious! The more knowledge the better judgement in the future I say.
Thank you!
This appears to answer a majority of the output in general but not the output that I have posted. Maybe I am not reading the right document?
Maybe not. Keep trying :) Seriously: what is it that you don't understand? Do you really want to know the meaning of every line in the sample you posted?
haha I honestly do want to know! I just hate getting information without knowing its purpose.
at least for these:
Number of Sequences: 0 Number of extensions: 40 Number of successful extensions: 2 Number of sequences better than 100000.0: 1 Number of HSP's better than 100000.0 without gapping: 1