Design gene-silencing oligos in one workspace, with NCBI isoform lookup, candidate generation, BLAST filtering, and record-ready exports.
ACGTGACT
Modules
Choose what you want to create
siRNA/shRNASearch NCBI isoforms or paste a sequence, generate siRNA candidates, filter transcript BLAST hits, and finalise order-ready shRNA oligos.
ASOSearch NCBI isoforms or paste a sequence, generate knockdown ASOs across a target position or span, and export scored candidates.
Exon-skipping ASOSelect a RefSeq isoform from NCBI, review exon/CDS structure, design splice-junction ASOs, and choose exon-skipping or NMD-focused exports.
Intron-retention ASODesign steric-blocking ASOs across selected introns, splice elements, or custom intronic intervals, with predicted coding and NMD consequences.
Scrambled controlsPaste existing oligos and generate matched scrambled negative controls with optional genome and transcript BLAST screening.
Oligo functional testingPaste oligos and predict likely target, binding region, mechanism, outcome, and off-target warnings from BLAST matches.
CRISPR guide RNAGuide RNA design and review module planned for future shCREATE releases.
More toolsA hub for additional oligo design workflows as the platform grows.
Current workflow
From target sequence to reviewable oligos
1. Select modelUse NCBI RefSeq isoforms or paste your own sequence.
2. Design and BLASTGenerate oligos, then screen against transcript or genome databases where appropriate.
3. Export recordsDownload the sequence model, candidate tables, BLAST outputs, summaries, and order-ready oligos.
General FAQ
About shCREATE+
What is shCREATE+?
shCREATE+ is a research-use oligo design workspace. It currently supports siRNA/shRNA, ASO knockdown, exon-skipping ASO, and intron-retention ASO design, and is being built as a home for CRISPR guide RNA and related modules.
Who is shCREATE+ for?
It is intended for academic and industry researchers who need a practical way to generate, review, filter, and export candidate oligos before experimental validation.
Is it suitable for clinical or diagnostic use?
No. shCREATE+ is research-use software. Outputs must be reviewed before ordering or experimental use and should not be treated as clinical, diagnostic, or therapeutic recommendations.
What information should I avoid submitting?
Do not submit confidential patient-identifiable information. Use public transcript sequences, non-identifiable research sequences, or synthetic examples where possible.
Why is there an access form?
The form helps understand who is testing the software, their institution type, and research interests, so the platform can be improved responsibly as more modules are added.
Which modules are available now?
The siRNA/shRNA, ASO knockdown, exon-skipping ASO, and intron-retention ASO pipelines are available now. CRISPR guide RNA and additional oligo design workflows are planned as future shCREATE+ modules.
Can collaborators use it from outside my network?
Yes. The public links are designed for collaborators to test remotely, with shcreate.org as the main address and shcreate.app as a backup route.
How should I cite shCREATE+?
Use the suggested acknowledgement on this page for now. A more formal citation can be added when the software or manuscript has a final citable record.
Technical FAQ
How the current pipelines work
Step-by-step guide
Select a model.Search NCBI RefSeq isoforms where available, or paste a sequence manually.
Generate candidates.Set target position/span or ASO module settings, then review the candidate table.
Run BLAST.Use transcript BLAST for mature-transcript off-targets and genome BLAST for exon or intron ASOs.
Review and export.Download each table you need for records, including model, exons, candidates, BLAST, summaries, and final oligos.
Save your work link.Create a 24-hour link if you need to return to the same workspace later.
What does the siRNA/shRNA pipeline create?
It generates candidate siRNAs around a target site or span, filters them with transcript-level BLAST results, and converts selected candidates into shRNA oligos for ordering.
When should I use a span instead of a single position?
Use a span when any candidate overlapping a region is acceptable, for example a functional domain, exon segment, or mutation-adjacent interval.
What do the BLAST cutoffs mean?
Minimum oligo coverage controls how much of the oligo must align, maximum mismatches limits tolerated differences, and maximum E-value is kept loose so short-oligo biology is driven mainly by coverage and mismatch review.
Why use NCBI isoforms?
NCBI RefSeq lookup reduces manual copy-paste errors and lets users choose the isoform they intend to target before generating oligos.
What is the NMD export option?
The exon-skipping pipeline predicts exon skips that may create a frameshift and premature stop codon. The intron-retention pipeline predicts retained-intron coding and NMD consequences where transcript architecture allows.
Does a passing candidate mean it is ready to order?
No. shCREATE+ is research-use software. Users should manually review BLAST hits, sequence context, target biology, and experimental suitability before ordering or using any oligo.
How long do saved work links last?
Saved workspace links are available for 24 hours so collaborators can reopen a design without storing old work indefinitely on the server.
Citation
Suggested acknowledgement
Suggested citationshCREATE+: a research-use workspace for siRNA/shRNA, ASO knockdown, exon-skipping ASO, and intron-retention ASO design with NCBI isoform lookup, BLAST filtering, and exportable review records. Available at shcreate.org.
shCREATE
Oligo design workspace
Ready
Temporary work linkSave this workspace for 24 hours and reopen it from the generated URL.
1. Design exon-skipping ASOsSearch NCBI RefSeq, choose an isoform, review exon-skip predictions, then generate splice-junction ASOs.
Load a gene to select a RefSeq isoform from NCBI.
0 exonsExon coordinates from the selected mature RefSeq transcript.
Exon
Start
End
Length
CDS relation
0 exon-skip predictionsFrameshift and premature-stop review for each exon skip.
Exon
Frame status
First stop
NMD classification
0 ASOsSet the objective and ASO design controls before sending candidates to BLAST.
ID
Exon
Region
Target sequence
ASO sequence
Length
GC
Score
NMD
2. BLAST and filterChoose genome-only or genome plus transcripts, then filter ASOs using biologically plausible hit thresholds and off-target tolerance.
Running BLASTPreparing ASOs
Use
Selection
ID
Off-targets
Status
3. Finalise: 0 final ASOsReview the final filtered ASOs and download the record-ready table.
ID
Exon
Region
ASO sequence
ASO score
Off-target score
Combined score
Off-target genes
Status
0 negative controls
Parent ID
Control ID
Scrambled sequence
GC
BLAST status
Notes
1. Target sequenceSearch NCBI RefSeq by default, or switch to your own FASTA/sequence.
0 candidates
ID
Sequence
Start
End
Length
GC
Running BLASTPreparing candidates
0 selected IDs
Use
Selection
ID
Off-targets
Status
0 final designs
ID
Target sequence
Reverse complement
shRNA fwd
shRNA rev
Length
GC
Score
0 negative controls
Parent ID
Control ID
Scrambled sequence
GC
BLAST status
Notes
Scrambled negative-control oligo generatorPaste existing oligos, generate matched scrambled controls, then optionally BLAST them as a separate negative-control table.
Running BLASTPreparing controls
0 negative controls
Parent ID
Parent sequence
Control ID
Scrambled sequence
Oligo type
Length
GC
BLAST scope
Genome status
Transcriptome status
Export-ready sequence
Notes/warnings
Oligo functional testingPaste oligos and generate computational predictions of target, binding region, mechanism, outcome, and off-target risk.
