proteogenomics

• 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.

 cargo build

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_ __    _ __    ___   | |_    ___    ___     __ _    ___   _ __     ___    _ __ ___   (_)   ___   ___
| '_ \  | '__|  / _ \  | __|  / _ \  / _ \   / _` |  / _ \ | '_ \   / _ \  | '_ ` _ \  | |  / __| / __|
| |_) | | |    | (_) | | |_  |  __/ | (_) | | (_| | |  __/ | | | | | (_) | | | | | | | | | | (__  \__ \
| .__/  |_|     \___/   \__|  \___|  \___/   \__, |  \___| |_| |_|  \___/  |_| |_| |_| |_|  \___| |___/
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hmm proteome analyze
************************************************
Author Gaurav Sablok,
Email: codeprog@icloud.com
************************************************

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

• To install windows version:

rustup component add llvm-tools
rustup target add x86_64-pc-windows-msvc
git clone https://github.com/IBCHgenomic/varlinker.git
cd ensemblcov
cargo xwin build --target x86_64-pc-windows-msvc

Gaurav Sablok
codeprog@icloud.com