KOnezumi-AID

KOnezumi-AID is the command-line tool to automate the gRNA design for multiplex KO mouse using Target-AID

Installation

Prerequisits

• Python 3.9 or later
• Unix-like environment (Linux, macOS, WSL2, etc.)

Installation🔨

From Bioconda (Recommended)

conda install -c conda-forge -c bioconda konezumiaid

From PyPI:

pip install KOnezumiAID

Required Packages (Not needed if installed via conda)

• bedtools

Follow the official instruction

• bowtie

Follow the official instruction

Input data set (e.g. Mus musculus mm39)

Locus information

refFlat.txt.gz from UCSC

genomic sequence

mm39.fa.gz from UCSC

Download scripts (bash)

mkdir -p data
wget -O - https://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/refFlat.txt.gz |
    gzip -dc > data/refFlat.txt
wget -O - https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.fa.gz |
    gzip -dc > data/mm39.fa

Usage

Create data set for KOnezumi-AID

konezumiaid preprocess <your refFlat.txt Path> <your mm39.fa Path>

Examples

konezumiaid preprocess data/refFlat.txt data/mm39.fa

Search candidate by gene symbol or transcript name (Refseq id)

KOnezumi-AID accepts a gene symbol or a transcript name.

• Search by gene symbol

You can obtain the gRNAs that are present in all transcript variants.

• Search by transcript name

You can obtain the transcript's gRNAs and access more information about the gRNAs.

• in_start_150bp: The gRNA is located in the first 150bp of the transcript or not.
• in_50bp_from_LEJ: The gRNA is located in the 50bp from the last exon junction or not.
• exon_index: the index of the exon where the gRNA is located.

konezumiaid <-n | --name> <gene symbol | transcript name>

Examples

• Search candidate by the gene symbol

  $konezumiaid -n Rp1
  PTC gRNA
                     seq
  0  ACAGGTTATGCAGTGTCCTGTGG
  1  ACGACACAGCATCACCAGGCTGG
  2  GCCAGGGCCGAGGGCGCCTGCGG
  3  ACAGTTTGGCGGCGTTCGGGTGG
  4  CCAGGGCCGAGGGCGCCTGCGGG
  Acceptor gRNA
  No Acceptor gRNA found.
  Donor gRNA
  No Donor gRNA found.

• Search candidate by the transcript name

$ konezumiaid -n NM_001370921
PTC gRNA
                        seq  in_start_150bp  in_50bp_from_LEJ
0   ACAGTTTGGCGGCGTTCGGGTGG            True             False
1   ACGACACAGCATCACCAGGCTGG           False             False
2   ACAGGTTATGCAGTGTCCTGTGG           False             False
3   ACAACCTGTCCTTCCAGGTAAGG           False             False
4   ACCAATCAGAACAATCCCACTGG           False             False
5   ACGAATGTATCTGAGGATTAAGG           False             False
6   TCAGGCCAATGTCACATTGTGGG           False             False
7   CTCAGGCCAATGTCACATTGTGG           False             False
8   CCAGGGCCGAGGGCGCCTGCGGG           False             False
9   GCCAGGGCCGAGGGCGCCTGCGG           False             False
10  TCCAGTGGGATTGTTCTGATTGG           False             False
11  CCAGTACTGGGATTTGTCACTGG           False             False
Acceptor gRNA
                       seq  exon_index
0  ACCTGGGATTGAAAGGAACAAGG          20
1  TCTGTTGGAGAAAAGCCCCATGG          22
2  ACCTGAAGAAAATGGAAAACAGG          23
Donor gRNA
                       seq  exon_index
0  TACCTTGCCCAAGTCCATCATGG           8
1  TTACCTCTCACAGGTGAAGATGG          22