Benchling supports CRISPR on 99 genomes — What should be 100?

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Victor Pontis

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Jul 25, 2016, 4:49:55 PM7/25/16

to Genome Engineering using CRISPR/Cas Systems

My name is Victor Pontis and I am an engineer at Benchling where we build free tools for life science research.

Benchling's CRISPR tool allows you to calculate on and off target scores in seconds, design homologous recombination templates, and find guides for base editor co-developed with David Liu's lab.

We recently improved our genome import process to be much faster and now we support 99 genomes from Arabidopsis to Zebrafish. If the genome of your favorite organism is not in Benchling, please reply to this post so we can support your research!

For genomes from Ensembl, NCBI, or EuPathDB, simply send us a link to the homepage of the genome you need. Examples below:

Is your genome not on Ensembl or NCBI? No worries! Send us a link for the Fasta (.fa, .fna, .fsa, .fasta) and GFF3 (.gff, .gff3) files for that genome. Examples below:

Check below to see if your favorite organism already on Benchling :)

Assembly Name        | Organism Name
===================================================================================
ASM24760v1           | Acetobacterium woodii DSM 1030
AmbMex13_14.1.0      | Ambystoma mexicanum
TAIR10               | Arabidopsis thaliana
GCA_000724485.1      | Bacillus methanolicus MGA3 (GCA_000724485.1)
GCA_000009045.1      | Bacillus subtilis subsp. subtilis str. 168
v1.0                 | Brachypodium distachyon
WBcel235             | Caenorhabditis elegans
WS220                | Caenorhabditis elegans
C_jacchus3.2.1       | Callithrix jacchus
Ca22                 | Candida albicans SC5314 (diploid)
Ca21                 | Candida albicans SC5314 (haploid)
CanFam3.1            | Canis lupus familiaris
GCA_000002595.2      | Chlamydomonas reinhardtii
ASM34735v1           | Claviceps purpurea 20.1
ASM876v1             | Clostridium acetobutylicum ATCC 824
GCA_000484505.1      | Clostridium autoethanogenum DSM 10061
ASM6358v1            | Clostridium botulinum A str. ATCC 3502
ASM14368v1           | Clostridium ljungdahlii DSM 13528
ASM80725v1           | Clostridium pasteurianum DSM 525 = ATCC 6013 (GCA_000807255)
ASM47399v1           | Clostridium saccharobutylicum DSM 13864
ASM34088v1           | Clostridium saccharoperbutylacetonicum N1-4(HMT)
ASM15508v1           | Clostridium sporogenes ATCC 15579
CriGri_1.0           | Cricetulus griseus CHO-K1
Zv9                  | Danio rerio
GRCz10               | Danio rerio
BDGP5                | Drosophila melanogaster
BDGP6                | Drosophila melanogaster
ASM97063v1           | Eragrostis tef
GCA_000005845.2      | Escherichia coli str. K-12 substr. MG1655
GCA_000152245.2      | Eubacterium limosum KIST612
Felis_catus_6.2      | Felis catus
RR                   | Fusarium graminearum
Galgal4              | Gallus gallus
ASM129536v1          | Geobacillus thermoglucosidasius DSM 2542
ASM18240v1           | Giardia intestinalis ATCC 50581
ASM49871v1           | Giardia intestinalis DH
GCA_000002435.1      | Giardia lamblia ATCC 50803
ASM18266v1           | Giardia lamblia P15
GRCh38               | Homo sapiens
GRCh37               | Homo sapiens
NCBI36               | Homo sapiens
082214v1             | Hordeum vulgare
PicPas_Mar2011       | Komagataella pastoris CBS 7435
LinfantumJPCM5       | Leishmania infantum JPCM5
LmajorFriedlin       | Leishmania major strain Friedlin
MacFas_5.0           | Macaca fascicularis
MMUL_1               | Macaca mulatta
MalDomGD1.0          | Malus domestica
GCA_001659605.1      | Manihot esculenta
MesAur1.0            | Mesocricetus auratus
MicOch1.0            | Microtus ochrogaster
ASM1310v1            | Moorella thermoacetica ATCC 39073
GRCm38               | Mus musculus
NCBIM37              | Mus musculus
NODShiLtJ_b38        | Mus musculus (NOD/ShiLtJ)
NODShiLtJ_b37        | Mus musculus (NOD/ShiLtJ)
GCF_000215625.1      | Mustela putorius furo
ASM20922v1           | Nematostella vectensis
TN90                 | Nicotiana tabacum
OryCun2.0            | Oryctolagus cuniculus
IRGSP-1.0            | Oryza sativa Japonica Group
HdrR                 | Oryzias latipes
Oar_v3.1             | Ovis aries
DSM365V1             | Paenibacillus polymyxa
Pmin_1.0             | Patiria miniata
ASM920v1             | Peptoclostridium difficile 630
ASM2710v1            | Peptoclostridium difficile R20291
ASM40151v2           | Piscirickettsia salmonis LF-89 = ATCC VR-1361
May_2010             | Plasmodium berghei
ASM276v1             | Plasmodium falciparum 3D7
GCA_000006765.1      | Pseudomonas aeruginosa PAO1
GCA_000009285.2      | Ralstonia eutropha H16
Rnor_6.0             | Rattus norvegicus
Rnor_5.0             | Rattus norvegicus
GCA_000012905.2      | Rhodobacter sphaeroides 2.4.1
ASM1456v1            | Rhodococcus jostii RHA1
R64-1-1              | Saccharomyces cerevisiae
ASM76626v2           | Saccharomyces cerevisiae SK1
Skow_1.1             | Saccoglossus kowalevskii
ASM15154v2           | Saprolegnia parasitica
ASM294v2             | Schizosaccharomyces pombe 972h-
GCA_000188115.2      | Solanum lycopersicum str. Heinz 1706
Sorbi1               | Sorghum bicolor
ASM15488v1           | Streptomyces sp. Mg1
Sscrofa10.2          | Sus scrofa
GCA_000012525.1      | Synechococcus elongatus PCC 7942
GCA_000019485.1      | Synechococcus sp. PCC 7002
GCA_000317085.1      | Synechococcus sp. PCC 7502
GCA_000009725.1      | Synechocystis sp. PCC 6803
TGGT1                | Toxoplasma gondii GT1
ToxoDB-7.1           | Toxoplasma gondii ME49
TgondiiRH            | Toxoplasma gondii RH
Tcas3                | Tribolium castaneum
TryBru_Apr2005_chr11 | Trypanosoma brucei
IGGP_12x             | Vitis vinifera
JGI_4.2              | Xenopus tropicalis
PO1f_A5_AB_scf       | Yarrowia lipolytica PO1f
AGPv3                | Zea mays
ASM710v1             | Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

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