https://github.com/sciencegenome/proteome-hmm
rust based hmm domain
https://github.com/sciencegenome/proteome-hmm
bioinformatics genome-analysis genome-annotation hmm hmm-model hmmer
Last synced: 4 months ago
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rust based hmm domain
- Host: GitHub
- URL: https://github.com/sciencegenome/proteome-hmm
- Owner: sciencegenome
- License: mit
- Created: 2025-01-29T20:11:51.000Z (5 months ago)
- Default Branch: main
- Last Pushed: 2025-01-31T19:02:05.000Z (5 months ago)
- Last Synced: 2025-01-31T19:24:01.723Z (5 months ago)
- Topics: bioinformatics, genome-analysis, genome-annotation, hmm, hmm-model, hmmer
- Language: Rust
- Homepage:
- Size: 21.5 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# proteome-hmm
- rust crate for hmm domain search, selection and annotation mapper.
- please see the last commit message and if it says compiled binary then it is completed or else still in development version.
```
cargo build
```
```
➜ proteome-hmm git:(main) ✗ ./target/debug/hmm-domain -h
hmm proteome analyze
Usage: hmm-domain
Commands:
target-hmm select the targets from the hmm
score-hmm select the scores from the hmm
evalue-hmm select the evalues from the hmm
eval-target select the targets based on evalue and target
targetcounts prepare the unique counts of the domains
help Print this message or the help of the given subcommand(s)
Options:
-h, --help Print help
-V, --version Print version
```
```
➜ proteome-hmm git:(main) ✗ ./target/debug/hmm-domain score-hmm ./sample-file/samplehmmalignment.txt 12.5
==> filtered-scores-with-all-targets.txt <==
HTH_26 63 WP_003872347.1 189 0.00000000000023 37.9 1 60 14 72 14 75 Cro/C1-type
HTH_24 48 WP_003872375.1 193 0.0000023 13.8 17 37 34 54 33 54 Winged
HTH_24 48 WP_003872469.1 148 0.00000000000000000054 55.1 1 48 4 51 4 51 Winged
HTH_24 48 WP_003872548.1 161 0.0000062 13.1 7 47 47 87 43 88 Winged
HTH_26 63 WP_003872666.1 178 0.00000000058 27.2 2 62 5 64 5 65 Cro/C1-type
==> filtered-score.txt <==
HTH_XRE 56 WP_003872292.1 132 0.00000003 20.9 17 56 35 75 35 75 -
HTH_XRE 56 WP_003872307.1 249 0.00000048 17.1 2 34 149 187 148 195 -
HTH_XRE 56 WP_003872347.1 189 0.0000000000000000000022 63.4 1 56 14 69 14 69 -
HTH_26 63 WP_003872347.1 189 0.00000000000023 37.9 1 60 14 72 14 75 Cro/C1-type
HTH_24 48 WP_003872375.1 193 0.0000023 13.8 17 37 34 54 33 54 Winged
```
```
./target/debug/hmm-domain target-hmm ./sample-file/samplehmmalignment.txt Winged
➜ proteome-hmm git:(main) ✗ head -n 3 filtered-target.txt
HTH_24 48 WP_003872375.1 193 0.0000023 13.8 17 37 34 54 33 54 Winged
HTH_24 48 WP_003872375.1 193 0.0000023 -3.9 23 31 180 188 178 189 Winged
HTH_24 48 WP_003872469.1 148 0.00000000000000000054 55.1 1 48 4 51 4 51 Winged
./target/debug/hmm-domain evalue-hmm ./sample-file/samplehmmalignment.txt 1.3e-5
==> ./sample-file/evalue-filter-with-all-targets.txt <==
HTH_XRE 56 210 WP_003872175.1 0.000023 10.9 3 30 10 56 8 84 -
HTH_XRE 56 210 WP_003872175.1 0.000023 -2.6 14 24 139 149 138 150 -
HTH_XRE 56 210 WP_003872175.1 0.000023 -3.4 44 53 187 196 185 198 -
HTH_24 48 253 WP_003872618.1 0.000016 11.5 22 47 43 68 42 69 Winged
==> ./sample-file/evalues-filter-with-target-annotated.txt <==
HTH_24 48 WP_003872618.1 0.000016 11.5 22 47 43 68 42 69 Winged
HTH_24 48 WP_003872618.1 0.000016 -3.9 32 39 117 124 116 127 Winged
HTH_24 48 WP_003872953.1 0.000023 10.1 19 43 47 71 41 72 Winged
HTH_24 48 WP_003872953.1 0.000023 -1.6 31 42 192 203 191 204 Winged
```
```
➜ proteome-hmm git:(main) ✗ ./target/debug/hmm-domain eval-target ./sample-file/samplehmmalignment.txt 1.3e-5 Winged
➜ proteome-hmm git:(main) ✗ head -n 3 evalue-filter-with-all-targets.txt
HTH_24 48 253 WP_003872618.1 0.000016 11.5 22 47 43 68 42 69 Winged
HTH_24 48 253 WP_003872618.1 0.000016 -3.9 32 39 117 124 116 127 Winged
HTH_24 48 245 WP_003872953.1 0.000023 10.1 19 43 47 71 41 72 Winged
./target/debug/hmm-domain eval-target ./sample-file/samplehmmalignment.txt 1.3e-5 Cro/C1-type
➜ proteome-hmm git:(main) ✗ head -n 1 evalue-filter-with-all-targets.txt
HTH_26 63 213 WP_003876921.1 0.000033 11.4 10 36 42 67 40 77 Cro/C1-type
```
```
➜ proteome-hmm git:(main) ✗ ./target/debug/hmm-domain targetcounts ./sample-file/samplehmmalignment.txt
The domain aligned targets for the enrichment are: {"Winged": 1, "Cro/C1-type": 1, "Domain": 1}
```
Gaurav Sablok