Creates custom gene-editing constructs developed by the
Niles Lab at MIT,
designed for knock-out or conditional knock-down in Plasmodium falciparum,
by delivering a 3' or 5' UTR post-transcriptional regulatory element payload to a specific given gene.
Command line interface and code available through
Use user-annotated homology regions and/or guide RNAs (if any):
Alternatively, you may
manually annotate all
CRISPR guide RNAs
to be included in targeting. Guide RNA annotations should start
with the word "gRNA" in the label, followed by
indicating their order of preference. You may also annotate
hand-picked left and right homologous regions on your file
(annotated with the words "LHR" and "RHR" in the label,
you do not want GeneTargeter to choose them automatically for you.
Extend gBlock if under minimum size (instead of using oligos):
Use HA tags (5' designs):
Provide a list of 3D7 gene IDs or upload a
annotated with the gene's sequence
in 5'->3' sense.
If you load your own files, make sure the target gene name in each
text box matches the gene's annotation on the plasmid.
GeneTargeter outputs seven kinds of files:
a GenBank file containing the given gene annotated with
the chosen left and right homologous regions, before chromosomal
a GenBank file containing the fully annotated plasmid
vector designed to target the given gene.
a GenBank file containing the edited chromosomal locus
targeted by the construct.
a CSV file containing primers and oligos designed to
assemble the new plasmid using
This file can be
imported into Benchling. Abbreviates primer names to fit on
commercial tube labels with the format:
Seven Digit Gene Identifier_Oligo type_Orientation
a FASTA file containing gene fragments with overlaps
designed to assemble the new plasmid using
a CSV file comparing different possible sgRNAs evaluated
by GeneTargeter before making a choice according to a variety of
scoring metrics, as well as the corresponding
recoded sgRNA for each in the final design.
a text file containing a message log and warnings
issued during the in silico design process, along with
plasmid assembly instructions.
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Submit gene IDs
List the gene IDs you want to target below (one ID per line):
On-target Cas9 gRNA scoring code and CFD scoring matrix obtained December 27, 2016 from Doench et al. (2016) supplementary material.
On-target Cas12 gRNA scoring coefficients obtained from Kim et al. (2017) supplementary material, equivalent to the CINDEL online tool. Exact on-target scores may vary between GeneTargeter and CINDEL due to minor differenes in gRNA free energy calculations.