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GDPR/RODO
Home
Analyze
Manual
FAQ
Contact
GDPR/RODO
transCRISPR
1
Step 1
Genome
2
Step 2
DNA motif
3
Step 3
Target regions
4
Step 4
Parameters
Genome:
-
Human Dec. 2013 (GRCh38/hg38)
Human Feb. 2009 (GRCh37/hg19)
Mouse Jun. 2020 (GRCm39/mm39)
Baboon Apr. 2017 (Panu_3.0/papAnu4)
Bonobo May 2020 (Mhudiblu_PPA_v0/panPan3)
C. elegans Feb. 2013 (WBcel235/ce11)
Cat Nov. 2017 (Felis_catus_9.0/felCat9)
Chicken Mar. 2018 (GRCg6a/galGal6)
Chimp Jan. 2018 (Clint_PTRv2/panTro6)
Cow Apr. 2018 (ARS-UCD1.2/bosTau9)
D. melanogaster Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)
Dog Oct. 2020 (Dog10K_Boxer_Tasha/canFam6)
Dog Mar. 2020 (UU_Cfam_GSD_1.0/canFam4)
Fugu Oct. 2011 (FUGU5/fr3)
Gorilla Aug. 2019 (Kamilah_GGO_v0/gorGor6)
Horse Jan. 2018 (EquCab3.0/equCab3)
Lizard May 2010 (Broad AnoCar2.0/anoCar2)
Marmoset March 2009 (WUGSC 3.2/calJac3)
Orangutan Jan. 2018 (Susie_PABv2/ponAbe3)
Pig Feb. 2017 (Sscrofa11.1/susScr11)
Rat Nov. 2020 (mRatBN7.2/rn7)
Rat Jul. 2014 (RGSC 6.0/rn6)
Rhesus Feb. 2019 (Mmul_10/rheMac10)
S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3)
Sheep Nov. 2015 (Oar_v4.0/oviAri4)
Turkey Nov. 2014 (Turkey_5.0/melGal5)
X. tropicalis Nov. 2019 (UCB_Xtro_10.0/xenTro10)
X. tropicalis Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9)
Zebra finch Feb. 2013 (WashU taeGut324/taeGut2)
Zebrafish May 2017 (GRCz11/danRer11)
Motif sequences
Motif sequence file
Motif matrix
Motif matrix file
Motifs sequences (fasta, coma separated):
Motifs sequences file (fasta):
Upload motif sequences file
Clear
Motifs matrix:
Motif matrix file:
Upload motif matrix file
Clear
Motif matrix format:
csv
tsv
xlsx
AlignAce output file format
Cluster Buster position frequency matrix format
XMS matrix format
MEME output file motif
MINIMAL MEME output file motif
TRANSFAC database file format
Generic position-frequency matrix format with four columns. (cisbp, homer, hocomoco, neph, tiffin)
Generic position-frequency matrix format with four row. (scertf, yetfasco, hdpi, idmmpmm, flyfactor survey)
JASPAR-style position-frequency matrix
JASPAR-style multiple PFM format
JASPAR-style sites file
Genome coordinates
Sequence as a text
Upload sequence file
Upload coordinates file
Chromosome (chr1, chr2, chrX etc.):
Coordinates start:
Coordinates end:
Search sequences (fasta, coma separated):
Upload sequence file
Clear
Upload coordinates file
Clear
Motif sequence mode:
D. R. Cavener rule set (recommended for motif)
Frequency for nucleotide greater or equal 5%
Frequency for nucleotide greater or equal 10%
Frequency for nucleotide greater or equal 15%
Frequency for nucleotide greater or equal 20%
Frequency for nucleotide greater or equal 25%
Select the most frequent nucleotides that cover at least 90%
Select the most frequent nucleotides that cover at least 85%
Select the most frequent nucleotides that cover at least 80%
PAM:
NGG Cas9 S. pyogenes
NGA Cas9 S. pyogenes
NGCG Cas9 S. pyogenes
Variants:
Cas9
dCas9
Custom
Define maximal distance (in bp) from the motif to PAM:
Off target mode:
Standard (up to 4 mismatches)
Rapid (up to 3 mismatches)
Email to send information when calculation finishes (optional):
Pursuant to art. 6 sec. 1 lit. a of the GDPR, I consent to the processing of my e-mail address by the Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań for contact purposes, in particular, notification of the completion of calculations to the e-mail address provided. This consent may be withdrawn at any time. Withdrawal of the consent does not affect the lawfulness of the processing which was carried out on the basis of consent before its withdrawal. Withdrawal of the consent will result in the fact that we will not be able to inform about the results via e-mail.
no demo
demo 3
LOAD EXAMPLE:
1
2
3
EXAMPLE FILES:
example_3_coordinates.txt
example_3_matrix.txt
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