DGD

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DGD (Deep Guide Designer)

DGD (Deep Guide Designer) is python based on-target scoring method for Cas9 sequences, which is developed by integrating information from target sequence, biofeatures and spacer-scaffold base-pairing of sgRNA into CNN based deep learning model.

Source Code

Briefings of python files

• Github directory contains main files and subsidary python files for the ease of users.
• Name of main file is DGD.py which when run will execute all the necessary files and give score as output.
• The input file should be fasta sequence (.fa), DGD pipeline can take multiple fasta sequence files.
• Accessory files (python) are provided for users in Accessory folder, who would like to study and integrate the features and outputs in their pipelines.
• Prior to use of any files both main and accessory, please install the packages as mentioned in Requirement section.

Requirements

• Python 3.6 or above
• Vienna RNA package
• Numpy (version >= 1.12.4)
• Pandas (version >= 1.1.4)
• Keras (version >= 2.2.5)
• Tensorflow(version == 2.2.0)
• R (version >= 3.6)
• gcc (version >= 4.7.0)

Package Installation

You compile c++ file:

make

Pre-compiled files(connection_to_matrix ) are provided for DGD.py

For Vienna RNA package see the instruction in their official site https://www.tbi.univie.ac.at/RNA/ for python installation The rest packages could be installed by using pip or conda

Use

DGD python files is executed on fasta file

• The input file should in fasta format
• For demo purpose the length of fasta file is in range between 100nt to 10000nt
• The output are shown in .csv format which compromises of ID,Start,End,Strand, 30nt sequence and on-target score

   python DGD.py input.fa
   
   Example file: input.fa
   
    >JQ277699.1 Ovis aries LIN28A (LIN28A) mRNA, complete cds
    ACCCCTTTGCCTCCGGACTTCTCTGGGGCCAGCAGCCGCCCAAGCGAGGGCCCGGGGCCGCGAGCTCAGC
    AGACTACCATGGGCTCTGTGTCAAACCAGCAGTTCGCAGGTGGCTGCGCTAAGGCGCCGGAGGAAGCGCC
    GGAGGAGGCGCCGGAGGACGCGGCCCGCGCGGCGGAGGAGCCGCAGCTGCTGCACGGTGCCGGCATCTGT
    AAGTGGTTCAACGTGCGCATGGGGTTCGGCTTCCTGTCCATGACCGCCCGCGCAGGGGTCGCGCTCGACC
    CCCCGGTGGATGTCTTTGTGCACCAGAGTAAGCTGCACATGGAGGGCTTCCGGAGCCTGAAGGAGGGGGA
    GGCTGTGGAGTTCACCTTTAAGAAGTCCGCCAAGGGCCTGGAATCTATCCGAGTCACCGGCCCTGGTGGG
    GTGTTCTGTATTGGGAGTGAAAGGCGGCCCAAAGGGAAGAATGTGCAGAAACGCAGATCAAAGGGAGACA
    GGTGCTACAACTGTGGAGGTCTAGACCATCATGCCAAGGAATGCAAACTGCCACCGCAGCCCAAGAAGTG
    CCATTTCTGCCAGAGCATCAGCCATATGGTAGCCTCGTGCCCACTGAAGGCCCAGCAAGCTCCCAGCTCC
    CAGGGAAAGCCAGCCTACTTTCGGGAGGAGGAAGAAGAGATCCATAGCTCTGCCATGCTCCCAGAGGCCC
    AGAATTGAAGCCACAGTGGGTGGGAGCTATCCTTTTGTGATCAGAAAGCTTTGAGGAGCAGCATCAATCG
    CCTTTGCCTTCGGACTTCTCCGGGGCCAGCAGCCGCCCGACCAGGGGCCCGGGGCCACGGGCTCAGCCGA
    CGACCATGGGCTCCGTGTCCAACCAGCAGTTTGCAGGTGGCTGCGCCAAGGCGGCAGAAGAGGCGCCCGA
    GGAGGCGCCGGAGGACGCGGCCCGGGCGGCGGACGAGCCTCAGCTGCTGCACGGTGCGGGCATCTGTAAG
    TGGTTCAACGTGCGCATGGGGTTCGGCTTCCTGTCCATGACCGCCCGCGCCGGGGTCGCGCTCGACCCCC
    CAGTGGATGTCTTTGTGCACCAGAGTAAGCTGCACATGGAAGGGTTCCGGAGCTTGAAGGAGGGTGAGGC
    AGTGGAGTTCACCTTTAAGAAGTCAGCCAAGGGTCTGGAATCCATCCGTGTCACCGGACCTGGTGGAGTA
    TTCTGTATTGGGAGTGAGAGGCGGCCAAAAGGAAAGAGCATGCAGAAGCGCAGATCAAAAGGAGACAGGT
    GCTACAACTGTGGAGGTCTAGATCATCATGCCAAGGAATGCAAGCTGCCACCCCAGCCCAAGAAGTGCCA

    >Q278699.2 Ovis aries 
    ACCCCTTTGCCTCCGGACTTCTCTGGGGCCAGCAGCCGCCCAAGCGAGGGCCCGGGGCCGCGAGCTCAGC
    AGACTACCATGGGCTCTGTGTCAAACCAGCAGTTCGCAGGTGGCTGCGCTAAGGCGCCGGAGGAAGCGCC
    GGAGGAGGCGCCGGAGGACGCGGCCCGCGCGGCGGAGGAGCCGCAGCTGCTGCACGGTGCCGGCATCTGT
    AAGTGGTTCAACGTGCGCATGGGGTTCGGCTTCCTGTCCATGACCGCCCGCGCAGGGGTCGCGCTCGACC
    CCCCGGTGGATGTCTTTGTGCACCAGAGTAAGCTGCACATGGAGGGCTTCCGGAGCCTGAAGGAGGGGGA
    GGCTGTGGAGTTCACCTTTAAGAAGTCCGCCAAGGGCCTGGAATCTATCCGAGTCACCGGCCCTGGTGGG
    GTGTTCTGTATTGGGAGTGAAAGGCGGCCCAAAGGGAAGAATGTGCAGAAACGCAGATCAAAGGGAGACA
    GGTGCTACAACTGTGGAGGTCTAGACCATCATGCCAAGGAATGCAAACTGCCACCGCAGCCCAAGAAGTG
    CCATTTCTGCCAGAGCATCAGCCATATGGTAGCCTCGTGCCCACTGAAGGCCCAGCAAGCTCCCAGCTCC
    CAGGGAAAGCCAGCCTACTTTCGGGAGGAGGAAGAAGAGATCCATAGCTCTGCCATGCTCCCAGAGGCCC
    AGAATTGAAGCCACAGTGGGTGGGAGCTATCCTTTTGTGATCAGAAAGCTTTGAGGAGCAGCATCAATCG
    CCTTTGCCTTCGGACTTCTCCGGGGCCAGCAGCCGCCCGACCAGGGGCCCGGGGCCACGGGCTCAGCCGA

• Output (DGD.csv)

ID	Start	End	Strand	Sequence	DGD
Q278699.2:1938:1968	1938	1968	-	TTTCCCTGGGAGCTGGGAGCTTGCTGGGCC	18.69614792
JQ277699.1:295:325	295	325	+	TTGTGCACCAGAGTAAGCTGCACATGGAGG	66.6506424
Q278699.2:295:325	295	325	+	TTGTGCACCAGAGTAAGCTGCACATGGAGG	66.6506424
Q278699.2:1625:1655	1625	1655	+	TTGTGCACCAGAGTAAGCTGCACATGGAGG	66.6506424
JQ277699.1:1062:1092	1062	1092	+	TTGTGCACCAGAGTAAGCTGCACATGGAAG	67.54428864
Q278699.2:1062:1092	1062	1092	+	TTGTGCACCAGAGTAAGCTGCACATGGAAG	67.54428864
JQ277699.1:859:889	859	889	-	TTGGCGCAGCCACCTGCAAACTGCTGGTTG	34.56448746
Q278699.2:859:889	859	889	-	TTGGCGCAGCCACCTGCAAACTGCTGGTTG	34.56448746
JQ277699.1:636:666	636	666	-	TTCTTCCTCCTCCCGAAAGTAGGCTGGCTT	47.40981674
Q278699.2:636:666	636	666	-	TTCTTCCTCCTCCCGAAAGTAGGCTGGCTT	47.40981674
Q278699.2:1966:1996	1966	1996	-	TTCTTCCTCCTCCCGAAAGTAGGCTGGCTT	47.40981674
JQ277699.1:1007:1037	1007	1037	+	TTCCTGTCCATGACCGCCCGCGCCGGGGTC	50.25638199
Q278699.2:1007:1037	1007	1037	+	TTCCTGTCCATGACCGCCCGCGCCGGGGTC	50.25638199
JQ277699.1:240:270	240	270	+	TTCCTGTCCATGACCGCCCGCGCAGGGGTC	60.52968216
Q278699.2:240:270	240	270	+	TTCCTGTCCATGACCGCCCGCGCAGGGGTC	60.52968216
Q278699.2:1570:1600	1570	1600	+	TTCCTGTCCATGACCGCCCGCGCAGGGGTC	60.52968216
JQ277699.1:607:637	607	637	-	TTCCCTGGGAGCTGGGAGCTTGCTGGGCCT	32.67510605
Q278699.2:607:637	607	637	-	TTCCCTGGGAGCTGGGAGCTTGCTGGGCCT	32.67510605
Q278699.2:1937:1967	1937	1967	-	TTCCCTGGGAGCTGGGAGCTTGCTGGGCCT	32.67510605
JQ277699.1:578:608	578	608	-	TTCAGTGGGCACGAGGCTACCATATGGCTG	59.14524078
Q278699.2:578:608	578	608	-	TTCAGTGGGCACGAGGCTACCATATGGCTG	59.14524078
Q278699.2:1908:1938	1908	1938	-	TTCAGTGGGCACGAGGCTACCATATGGCTG	59.14524078
JQ277699.1:679:709	679	709	-	TTCAATTCTGGGCCTCTGGGAGCATGGCAG	52.64225006
Q278699.2:679:709	679	709	-	TTCAATTCTGGGCCTCTGGGAGCATGGCAG	52.64225006
Q278699.2:2009:2039	2009	2039	-	TTCAATTCTGGGCCTCTGGGAGCATGGCAG	52.64225006
JQ277699.1:92:122	92	122	-	TTAGCGCAGCCACCTGCGAACTGCTGGTTT	19.55876541
Q278699.2:92:122	92	122	-	TTAGCGCAGCCACCTGCGAACTGCTGGTTT	19.55876541
Q278699.2:1422:1452	1422	1452	-	TTAGCGCAGCCACCTGCGAACTGCTGGTTT	19.55876541
JQ277699.1:86:116	86	116	+	TGTGTCAAACCAGCAGTTCGCAGGTGGCTG	55.41802216

License

MIT

Contributors

A. Vipin Menon, Jang-il Sohn, Seokju Park and Jin-Wu Nam

Bioinformatic and Genomics Lab., Hanyang University, Seoul 04763, Korea

Contact

If you have any issues, please contact us

Principal Investigator

Jin-Wu Nam (jwnam@hanyang.ac.kr)

if he is unavailable, please email

A. Vipin Menon (a.vipin.menon@gmail.com)