Closed AlisaGU closed 1 year ago
Because it's not statistically significant when it's in the much larger sequence. When you've got 10M-fold more places to find a domain, the E-value is ~10M-fold higher.
Hi, the result was still empty, even the reported evalue was set to 10000000000.
hmmsearch -o /dev/null --domtblout 10M.dom -E 10000000000 --domE 10000000000 --noali KRAB.hmm a.fa
[test_10m]$ cat 10M.dom
# --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord
# target name accession tlen query name accession qlen E-value score bias # of c-Evalue i-Evalue score bias from to from to from to acc description of target
#------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------
#
# Program: hmmsearch
# Version: 3.3 (Nov 2019)
# Pipeline mode: SEARCH
# Query file: KRAB.hmm
# Target file: a.fa
# Option settings: hmmsearch -o /dev/null --domtblout 10M.dom --noali -E 10000000000 --domE 10000000000 KRAB.hmm a.fa
# Current dir: test_10m
# Date: Sat Apr 8 20:36:38 2023
# [ok]
Because of the way the acceleration filter methods work in HMMER3, it is generally unable to identify insignificant high E-value hits, no matter what you set -E and --domE to (and you generally wouldn't want to identify a lot of false positives, either).
Thanks for your quick answer. Actually, I used hmmer to search domains against a translated genome. It seems that domains were unlikely to be detected in a longer sequence. To get a more precise result, what is the optimal length to split genome for you?
You should translate into proteins/ORFs. HMMER makes assumptions about what proteins typically look like, and how long they are. If you're just "translating" a long genome sequence into only six "open reading frames", with * for stops or something, that's not going to work well.
See http://cryptogenomicon.org/hmmscan-vs-hmmsearch-speed-the-numerology.html for some more information.
This link you shared is especially useful when I choose the program between hmmscan and hmmsearch. Thanks for your advice~
Hi, When I use hmmsearch to search domain in sequence 10M long, the program returned a blank list.
However, when the domain was against the subsequence of a.fa, a hit was found.
Do you know what the reason is? And, what should I do to detect this hit in a.fa?
Best regards,