- rust crate for hmm domain search, selection and annotation mapper.
- it reports only chains with atoms for the id and sequence and euclidean distance for all irrespective of chain and atoms.
- Euclidean distance chain comparsion for two point coordinate protein.
- Euclidean distance chain coordinate comparsion for all protein atoms of the chain.
- please see the last commit message and if it says compiled binary then it is completed or else still in development version.
cargo build
gauravsablok@genome proteome-hmm main ? ./target/debug/proteogenomics -h
proteome analyzers
Usage: proteogenomics <COMMAND>
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
pdb-id
pdb-sequence extract the sequence of the pdf file
euclidean-comparative calculate the euclidean distance bettwen two chain coordinates
euclidean-all calculates the euclidean distance for all chain atoms
help Print this message or the help of the given subcommand(s)
Options:
-h, --help Print help
-V, --version Print version
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-hmm ./sample-file/samplehmmalignment.txt Winged
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
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
eval-target ./sample-file/samplehmmalignment.txt 1.3e-5 Winged
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
eval-target ./sample-file/samplehmmalignment.txt 1.3e-5 Cro/C1-type
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
targetcounts ./sample-file/samplehmmalignment.txt
The domain aligned targets for the enrichment are: {"Winged": 1, "Cro/C1-type": 1, "Domain": 1}
euclidean-comparative sample.pdb A 10 10 N CA
The eucledian distance between to given coordinates of the same chain is 1.4656264
euclidean-comparative sample.pdb A 1 1 N CA
The eucledian distance between to given coordinates of the same chain is 1.4909409
euclidean-all sample.pdb A
The vector containing the eucleadian distance for those chain atoms are:
[1.4909409, 1.5401275, 1.254727, 3.479588, 1.4994173, 1.4884146 ...]
and will write a eucledian file as
32.231 15.281 -13.143 32.184 14.697 -11.772 1.4909409
32.184 14.697 -11.772 33.438 13.89 -11.387 1.5401275
33.438 13.89 -11.387 34.102 13.07 -12.066 1.254727
34.102 13.07 -12.066 30.797 14.065 -11.625 3.479588
30.797 14.065 -11.625 30.976 12.589 -11.819 1.4994173
30.976 12.589 -11.819 29.608 12.016 -11.694 1.4884146
29.608 12.016 -11.694 28.942 12.335 -12.945 1.4526931
28.942 12.335 -12.945 27.67 12.696 -13.05 1.3263968
27.67 12.696 -13.05 26.901 12.777 -11.999 1.3048087
26.901 12.777 -11.999 27.161 12.963 -14.255 2.2785378
Gaurav Sablok