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scan potential FN seqeuences
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jayhesselberth committed Aug 19, 2024
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6 changes: 6 additions & 0 deletions results/2024-08-24/run.sh
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#! /usr/bin/env bash

awk '{print ">"$1"\n"$2}' < seqs.tsv > seqs.faa

hmmsearch --max --tblout seqs.class-1.tab ../../curated-models/2A-class-1.hmm seqs.faa > seqs.class-1.hmmsearch
hmmsearch --max --tblout seqs.class-2.tab ../../curated-models/2A-class-2.hmm seqs.faa > seqs.class-2.hmmsearch
415 changes: 415 additions & 0 deletions results/2024-08-24/seqs.class-1.hmmsearch
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32 changes: 32 additions & 0 deletions results/2024-08-24/seqs.class-1.tab
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# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target
#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- ---------------------
CR1-8_NV - 2A-class-1 - 9.1e-06 16.1 0.6 9.1e-06 16.1 0.6 2.0 3 0 0 3 3 3 1 -
CR1-18_BF - 2A-class-1 - 0.00017 12.0 0.2 0.00026 11.4 0.2 1.4 1 0 0 1 1 1 1 -
CR1-3_BF - 2A-class-1 - 0.00017 12.0 0.2 0.00026 11.4 0.2 1.4 1 0 0 1 1 1 1 -
STR-61_SP - 2A-class-1 - 0.00018 12.0 3.6 0.0013 9.2 3.6 1.9 1 1 0 1 1 1 1 -
CR1-19_NV - 2A-class-1 - 0.00031 11.2 2.0 0.00031 11.2 2.0 1.9 2 0 0 2 2 2 1 -
CR1-21_NV - 2A-class-1 - 0.00033 11.1 0.2 0.00033 11.1 0.2 2.7 3 0 0 3 3 3 1 -
L2-2_XT - 2A-class-1 - 0.00045 10.7 1.0 0.00045 10.7 1.0 2.7 3 0 0 3 3 3 1 -
CR1-2_NV - 2A-class-1 - 0.00055 10.4 11.9 0.00035 11.0 2.2 2.7 2 1 0 2 2 2 1 -
Crack-28_BF - 2A-class-1 - 0.00061 10.3 0.3 0.00061 10.3 0.3 2.2 2 0 0 2 2 2 1 -
Crack-10_BF - 2A-class-1 - 0.00084 9.8 0.5 0.0013 9.2 0.5 1.4 1 0 0 1 1 1 1 -
DHV-1 - 2A-class-1 - 0.002 8.6 4.5 0.0036 7.8 4.5 1.5 1 0 0 1 1 1 1 -
STR-32_SP - 2A-class-1 - 0.004 7.6 11.7 0.044 4.4 11.7 2.0 1 1 0 1 1 1 0 -
CR1-17_BF - 2A-class-1 - 0.021 5.4 7.7 0.0013 9.2 0.5 2.1 2 0 0 2 2 2 0 -
L2-3_XT - 2A-class-1 - 0.021 5.3 8.2 0.012 6.1 0.1 2.1 2 0 0 2 2 2 0 -
STR-55_SP - 2A-class-1 - 0.024 5.2 8.0 0.27 1.8 8.0 2.1 1 1 0 1 1 1 0 -
CR1-31_BF - 2A-class-1 - 0.042 4.4 5.0 0.084 3.5 5.0 1.5 1 0 0 1 1 1 0 -
L2-4_XT - 2A-class-1 - 0.37 1.4 13.4 0.017 5.6 1.3 2.5 2 0 0 2 2 2 0 -
STR-197_SP - 2A-class-1 - 0.42 1.2 10.7 0.053 4.1 0.2 2.2 2 0 0 2 2 2 0 -
CR1-L2-1_XT - 2A-class-1 - 1 0.0 15.1 0.017 5.6 1.4 2.6 2 1 0 2 2 2 0 -
#
# Program: hmmsearch
# Version: 3.4 (Aug 2023)
# Pipeline mode: SEARCH
# Query file: ../../curated-models/2A-class-1.hmm
# Target file: seqs.faa
# Option settings: hmmsearch --tblout seqs.class-1.tab --max ../../curated-models/2A-class-1.hmm seqs.faa
# Current dir: /Users/jayhesselberth/devel/2a-peptide-search/results/2024-08-24
# Date: Mon Aug 19 15:31:42 2024
# [ok]
311 changes: 311 additions & 0 deletions results/2024-08-24/seqs.class-2.hmmsearch
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# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.4 (Aug 2023); http://hmmer.org/
# Copyright (C) 2023 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: ../../curated-models/2A-class-2.hmm
# target sequence database: seqs.faa
# per-seq hits tabular output: seqs.class-2.tab
# Max sensitivity mode: on [all heuristic filters off]
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query: 2A-class-2 [M=24]
Description: 2A peptide (class 2)
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
4.8e-11 32.4 0.3 6.4e-11 32.0 0.3 1.2 1 DHV-1
1.2e-05 15.2 0.1 1.3e-05 15.1 0.1 1.2 1 STR-32_SP
6.1e-05 12.9 0.0 7.3e-05 12.7 0.0 1.2 1 STR-61_SP
0.00011 12.1 0.2 0.00016 11.6 0.2 1.3 1 STR-197_SP
0.00016 11.6 1.5 0.00019 11.3 1.5 1.1 1 CR1-17_BF
0.00045 10.2 0.2 0.00063 9.7 0.2 1.4 1 STR-55_SP
0.00053 9.9 0.1 0.00065 9.6 0.1 1.2 1 L2-4_XT
0.00058 9.8 0.1 0.00065 9.6 0.1 1.2 1 L2-3_XT
0.00061 9.7 0.1 0.00065 9.6 0.1 1.1 1 CR1-L2-1_XT
0.0011 8.9 0.0 0.0011 8.9 0.0 1.1 1 L2-2_XT
0.0013 8.7 0.1 0.0015 8.5 0.1 1.2 1 Crack-28_BF
0.0022 8.0 5.4 0.00045 10.2 2.3 1.5 2 Crack-10_BF
0.0034 7.3 0.1 0.0045 6.9 0.1 1.2 1 CR1-18_BF
0.0034 7.3 0.1 0.0045 6.9 0.1 1.2 1 CR1-3_BF
0.0086 6.0 4.9 0.012 5.6 4.9 1.2 1 CR1-31_BF
------ inclusion threshold ------
0.032 4.2 0.0 0.039 4.0 0.0 1.2 1 CR1-2_NV
0.038 4.0 0.1 0.066 3.2 0.1 1.4 1 CR1-8_NV
0.07 3.1 0.9 0.1 2.6 0.9 1.3 1 CR1-21_NV
0.44 0.6 0.1 0.62 0.1 0.1 1.3 1 CR1-19_NV


Domain annotation for each sequence (and alignments):
>> DHV-1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 32.0 0.3 6.4e-11 6.4e-11 6 19 .. 17 30 .] 16 30 .] 0.95

Alignments for each domain:
== domain 1 score: 32.0 bits; conditional E-value: 6.4e-11
xxxxxxxxxxxxxx RF
2A-class-2 6 RDLTeEGIEPNPGP 19
DLT EG+EPNPGP
DHV-1 17 KDLTTEGVEPNPGP 30
7************* PP

>> STR-32_SP
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 15.1 0.1 1.3e-05 1.3e-05 12 19 .. 22 30 .] 18 30 .] 0.89

Alignments for each domain:
== domain 1 score: 15.1 bits; conditional E-value: 1.3e-05
x.xxxxxxx RF
2A-class-2 12 G.IEPNPGP 19
G +EPNPGP
STR-32_SP 22 GoVEPNPGP 30
779****** PP

>> STR-61_SP
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 12.7 0.0 7.3e-05 7.3e-05 8 19 .. 18 30 .] 18 30 .] 0.85

Alignments for each domain:
== domain 1 score: 12.7 bits; conditional E-value: 7.3e-05
xxxxx.xxxxxxx RF
2A-class-2 8 LTeEG.IEPNPGP 19
L +G + PNPGP
STR-61_SP 18 LMTCGdVDPNPGP 30
567899******* PP

>> STR-197_SP
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 11.6 0.2 0.00016 0.00016 11 19 .. 21 30 .] 18 30 .] 0.84

Alignments for each domain:
== domain 1 score: 11.6 bits; conditional E-value: 0.00016
xx.xxxxxxx RF
2A-class-2 11 EG.IEPNPGP 19
+G I PNPGP
STR-197_SP 21 CGdINPNPGP 30
788******* PP

>> CR1-17_BF
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 11.3 1.5 0.00019 0.00019 13 19 .. 24 30 .] 21 30 .] 0.91

Alignments for each domain:
== domain 1 score: 11.3 bits; conditional E-value: 0.00019
xxxxxxx RF
2A-class-2 13 IEPNPGP 19
I+PNPGP
CR1-17_BF 24 IHPNPGP 30
9****** PP

>> STR-55_SP
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 9.7 0.2 0.00063 0.00063 12 19 .. 22 30 .] 18 30 .] 0.83

Alignments for each domain:
== domain 1 score: 9.7 bits; conditional E-value: 0.00063
x.xxxxxxx RF
2A-class-2 12 G.IEPNPGP 19
G + PNPGP
STR-55_SP 22 GdVNPNPGP 30
5589***** PP

>> L2-4_XT
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 9.6 0.1 0.00065 0.00065 12 19 .. 22 30 .] 18 30 .] 0.81

Alignments for each domain:
== domain 1 score: 9.6 bits; conditional E-value: 0.00065
x.xxxxxxx RF
2A-class-2 12 G.IEPNPGP 19
G I PNPGP
L2-4_XT 22 GdISPNPGP 30
5588***** PP

>> L2-3_XT
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 9.6 0.1 0.00065 0.00065 12 19 .. 22 30 .] 18 30 .] 0.81

Alignments for each domain:
== domain 1 score: 9.6 bits; conditional E-value: 0.00065
x.xxxxxxx RF
2A-class-2 12 G.IEPNPGP 19
G I PNPGP
L2-3_XT 22 GdISPNPGP 30
5588***** PP

>> CR1-L2-1_XT
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 9.6 0.1 0.00065 0.00065 12 19 .. 22 30 .] 18 30 .] 0.81

Alignments for each domain:
== domain 1 score: 9.6 bits; conditional E-value: 0.00065
x.xxxxxxx RF
2A-class-2 12 G.IEPNPGP 19
G I PNPGP
CR1-L2-1_XT 22 GdISPNPGP 30
5588***** PP

>> L2-2_XT
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 8.9 0.0 0.0011 0.0011 13 19 .. 24 30 .] 18 30 .] 0.79

Alignments for each domain:
== domain 1 score: 8.9 bits; conditional E-value: 0.0011
xxxxxxx RF
2A-class-2 13 IEPNPGP 19
+ PNPGP
L2-2_XT 24 VSPNPGP 30
77***** PP

>> Crack-28_BF
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 8.5 0.1 0.0015 0.0015 13 19 .. 24 30 .] 19 30 .] 0.84

Alignments for each domain:
== domain 1 score: 8.5 bits; conditional E-value: 0.0015
xxxxxxx RF
2A-class-2 13 IEPNPGP 19
+ PNPGP
Crack-28_BF 24 VSPNPGP 30
66***** PP

>> Crack-10_BF
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -2.5 0.1 3.9 3.9 8 11 .. 7 10 .. 7 11 .. 0.77
2 ! 10.2 2.3 0.00045 0.00045 13 19 .. 24 30 .] 23 30 .] 0.94

Alignments for each domain:
== domain 1 score: -2.5 bits; conditional E-value: 3.9
xxxx RF
2A-class-2 8 LTeE 11
LTe
Crack-10_BF 7 LTEQ 10
8996 PP

== domain 2 score: 10.2 bits; conditional E-value: 0.00045
xxxxxxx RF
2A-class-2 13 IEPNPGP 19
I+PNPGP
Crack-10_BF 24 IHPNPGP 30
9****** PP

>> CR1-18_BF
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 6.9 0.1 0.0045 0.0045 14 19 .. 25 30 .] 23 30 .] 0.93

Alignments for each domain:
== domain 1 score: 6.9 bits; conditional E-value: 0.0045
xxxxxx RF
2A-class-2 14 EPNPGP 19
E NPGP
CR1-18_BF 25 ETNPGP 30
99**** PP

>> CR1-3_BF
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 6.9 0.1 0.0045 0.0045 14 19 .. 25 30 .] 23 30 .] 0.93

Alignments for each domain:
== domain 1 score: 6.9 bits; conditional E-value: 0.0045
xxxxxx RF
2A-class-2 14 EPNPGP 19
E NPGP
CR1-3_BF 25 ETNPGP 30
99**** PP

>> CR1-31_BF
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 5.6 4.9 0.012 0.012 14 19 .. 25 30 .] 25 30 .] 0.98

Alignments for each domain:
== domain 1 score: 5.6 bits; conditional E-value: 0.012
xxxxxx RF
2A-class-2 14 EPNPGP 19
EPNPGP
CR1-31_BF 25 EPNPGP 30
9***** PP

>> CR1-2_NV
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 4.0 0.0 0.039 0.039 16 19 .. 27 30 .] 19 30 .] 0.85

Alignments for each domain:
== domain 1 score: 4.0 bits; conditional E-value: 0.039
xxxx RF
2A-class-2 16 NPGP 19
NPGP
CR1-2_NV 27 NPGP 30
***9 PP

>> CR1-8_NV
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 3.2 0.1 0.066 0.066 13 18 .. 23 28 .. 21 28 .. 0.83

Alignments for each domain:
== domain 1 score: 3.2 bits; conditional E-value: 0.066
xxxxxx RF
2A-class-2 13 IEPNPG 18
+E NPG
CR1-8_NV 23 VELNPG 28
999**9 PP

>> CR1-21_NV
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 2.6 0.9 0.1 0.1 16 19 .. 27 30 .] 22 30 .] 0.92

Alignments for each domain:
== domain 1 score: 2.6 bits; conditional E-value: 0.1
xxxx RF
2A-class-2 16 NPGP 19
NPGP
CR1-21_NV 27 NPGP 30
9*** PP

>> CR1-19_NV
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 0.1 0.1 0.62 0.62 17 19 .. 28 30 .] 21 30 .] 0.84

Alignments for each domain:
== domain 1 score: 0.1 bits; conditional E-value: 0.62
xxx RF
2A-class-2 17 PGP 19
PGP
CR1-19_NV 28 PGP 30
999 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (24 nodes)
Target sequences: 19 (569 residues searched)
Passed MSV filter: 19 (1); expected 19.0 (1)
Passed bias filter: 19 (1); expected 19.0 (1)
Passed Vit filter: 19 (1); expected 19.0 (1)
Passed Fwd filter: 19 (1); expected 19.0 (1)
Initial search space (Z): 19 [actual number of targets]
Domain search space (domZ): 19 [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 25.72
//
[ok]
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