bretonics / CHOMP

Search guide-RNA sequences given a genome or gene sequence

CHOMP 🐊

CRISPR Tool

CHOMP will search for all 'n' window sized guide RNAs (gRNAs) sequences containing an NGG at the tail end. Default window size is 23.

ex.) ATGTAGCTAGCTAGCTAGTAGGG.

It will report how many occurrences of this sequence are present in the target sequence (off-target sites), along with number of matching bases for each subject/query hit. You can use that to determine which gRNAs you may want to use as CRISPR target(s).

Run CHOMP

perl chomp.pl -seq usr/test.fasta -out gRNAs

Arguments

-seq                Sequence file to search gRNAs [required]
-genome             Genome sequence file(s) to BLAST search (search instead of -seq)
-down               Down sequence to append
-up                 Up sequence to append
-window             Window size for gRNA oligo (default = 23)
-ss                 Secondary structure prediction
-out                Out file name [required]
-outdir             Out directory name
-help               Shows this message

Output

Writes 2 files under the default directory gRNAs:

'.fasta'

Fasta file of each gRNA sequence found.

>gRNA_0:0
ATGTAGCTAGCTAGCTAGTAGGG
>gRNA_1:23
AAAAAATTTTCTCTATCTAACGG
>gRNA_2:24
AAAAATTTTCTCTATCTAACGGG
>gRNA_3:115
TGTGATCACGTACTATTATGCGG
>gRNA_4:149
AAAAATCCCATCGATCTAGCAGG
>gRNA_5:154
TCCCATCGATCTAGCAGGCCCGG
.
.
.
>gRNA_16:99
ATAGTACGTGATCACAGTCATGG

Suffix digit after ':' denotes nucleotide position in sequence where gRNA was found. Ex.) gRNA_16:99 , gRNA was found starting at nucleotide position 99 in -seq sequence.

'.txt'

Report with each gRNA sequence's details.

CHOMP will report how many occurrences of this sequence are present in the target sequence (off-target sites), along with the number of base pair matches (identities) for each. You can use this to determine which gRNA sequence is best to use for target.

Name	Sequence	Strand	Palindrome	Subject	Start	Occurrences	Identities
gRNA_13	TCGTCATGCATGCTCGCTCCGGG	reverse	No	test	173	1	8
gRNA_12	TTCGTCATGCATGCTCGCTCCGG	reverse	No	test	174	1	8
gRNA_3	TGTGATCACGTACTATTATGCGG	plus	No	test	116	2	8
gRNA_16	ATAGTACGTGATCACAGTCATGG	reverse	No	test	109	2	8
gRNA_8	AAAAAAAATTTTCCCTATCGGGG	plus	No	test	195	1	9
gRNA_7	GAAAAAAAATTTTCCCTATCGGG	plus	No	test	194	1	9
gRNA_6	CGAAAAAAAATTTTCCCTATCGG	plus	No	test	193	1	9
gRNA_9	AAAAAAATTTTCCCTATCGGGGG	plus	No	test	196	1	9
gRNA_4	AAAAATCCCATCGATCTAGCAGG	plus	No	test	150	6	11,9,7
gRNA_0	ATGTAGCTAGCTAGCTAGTAGGG	plus	No	test	1	4	14,12,10
gRNA_2	AAAAATTTTCTCTATCTAACGGG	plus	No	test	25	3	15,10,8
gRNA_15	TCCGGGCCTGCTAGATCGATGGG	reverse	No	test	156	6	15,9,7
gRNA_14	CTCCGGGCCTGCTAGATCGATGG	reverse	No	test	157	6	15,9,7
gRNA_5	TCCCATCGATCTAGCAGGCCCGG	plus	No	test	155	6	15,9,7
gRNA_1	AAAAAATTTTCTCTATCTAACGG	plus	No	test	24	3	16,10,8
gRNA_11	TATAGCATGGGCCCCCGATAGGG	reverse	No	test	207	1	23
gRNA_10	CTATAGCATGGGCCCCCGATAGG	reverse	No	test	208	1	23

Table is sorted in increasing order using the top identity for each gRNA sequence, and then sorted by number of occurrences, in current subject.