FancyGene statistics

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Popular tool citations

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FancyGene specifications

Information


Unique identifier OMICS_04278
Name FancyGene
Interface Web user interface
Restrictions to use None
Input format GFF,GTF
Output format PNG,PDF
Programming languages Javascript, Perl
Computer skills Basic
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Publication for FancyGene

FancyGene in pipelines

 (5)
2016
PMCID: 5020681
PMID: 27679642
DOI: 10.3389/fpls.2016.01353

[…] coding sequence (cds) was amplified using b. napus cultivar zhongshuang no.9 cdna as the template and sequenced. to illustrate the structure of intron, exon and vit domain of the candidate genes, fancygene database was used to draw the gene structure according to the full-length genome from genoscope genome database and coding sequence from sequencing. the sequences of candidate genes […]

2013
PMCID: 3724490
PMID: 23663308
DOI: 10.1186/1471-2164-14-317

[…] subcellular localization was predicted using targetp 1.0 [] . gene structures of t. urticae abcs were visualized using the coordinates of each t. urticae abc transporter (available at []) and the fancygene visualization software []. n-glycosylation sites were predicted with netnglyc1.0 server []. only n-glycosylation sites with a “potential” score > 0.5 and with a jury agreement (“++”-sign […]

2013
PMCID: 3774814
PMID: 24066188
DOI: 10.1371/journal.pone.0075888

[…] nested race pcr with pcr anchor primer or generacertm 5′ nested primer. for real-time pcr, 8843-1 primer pair is specific against 3’ region of agaqp1a, and 8843-2 primer pair is against 3’ agaqp1b., fancygene [] was used to present gene structures on the genome. alignments of amino-acid sequences were performed using clustalw []. prediction of transmembrane domains was performed using the tmhmm […]

2012
PMCID: 3280228
PMID: 22355416
DOI: 10.1371/journal.pone.0032153

[…] from the alignments of their coding sequences to the corresponding genomic sequences using the est2genome program . the diagrams of exon-intron structures were obtained using the online program fancygene ., tandem duplications of aldh genes in the grape genome were identified by checking their physical locations in individual chromosomes. tandem duplicated genes were defined as adjacent […]

2011
PMCID: 3181264
PMID: 21980438
DOI: 10.1371/journal.pone.0025385

[…] coding sequences were aligned with the corresponding sequences in the p. vampyrus genome. intron-exon maps of the genes were drawn using fancy gene v1.4 (http://host13.bioinfo3.ifom-ieocampus.it/fancygene/). putative protein sequences for bat ifnλr1 and il10r2 were compared with sequences in the genbank database using the blastp algorithm . sequence alignments were performed using […]


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FancyGene in publications

 (30)
PMCID: 5636884
PMID: 29021633
DOI: 10.1038/s41598-017-13474-1

[…] and then aligned using clustal w,. the alternatively spliced ecr isoforms were discovered based on ecr gene sequence alignment. the ecr gene structure of different isoforms was described by fancygene software., the three-dimensional structures of the four isoforms were modelled with the online automated build homology model program at phyre2 using the crystal structure of the liganded […]

PMCID: 5514110
PMID: 28717173
DOI: 10.1038/s41598-017-06120-3

[…] accessions and 190,656 indels predicted between heinz and micro-tom genomes were used as training and truth set in variantrecalibrator. snps and indels along candidate genes were drawn using the fancygene v1.4 tool., snpeff was used to annotate and predict the effects of variants on genes in order to guide downstream analysis., predictsnp and provean were used to predict possible impact […]

PMCID: 5042409
PMID: 27685863
DOI: 10.1371/journal.pone.0163647

[…] on the seven chromosomes., the exon-intron organization of the fvmrlk genes was determined using plaza (http://bioinformatics.psb.ugent.be/plaza/). the fancy gene online tool (http://bio.ieo.eu/fancygene/) was used to illustrate the exon-intron structure of the fvmrlks []. the expectation maximization for motif elicitation online program (http://meme-suite.org/) [] for dna and protein […]

PMCID: 5020681
PMID: 27679642
DOI: 10.3389/fpls.2016.01353

[…] coding sequence (cds) was amplified using b. napus cultivar zhongshuang no.9 cdna as the template and sequenced. to illustrate the structure of intron, exon and vit domain of the candidate genes, fancygene database was used to draw the gene structure according to the full-length genome from genoscope genome database and coding sequence from sequencing. the sequences of candidate genes […]

PMCID: 5005469
PMID: 27610237
DOI: 10.1038/hortres.2016.42

[…] vvidofl24 and vvidofl25) not had their predicted subcellular location to the nucleus (). finally, intron and exon structures, as well as dof domains, were determined and are displayed in using fancygene v1.4., the 25 putative dof genes were found to be distributed in 14 out of the 19 grapevine chromosomes, as well as in the unplaced contigs chromosome (chrun), which contains sequences […]


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FancyGene institution(s)
Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Milan, Italy
FancyGene funding source(s)
Supported by AIRC and Cariplo Grants.

FancyGene reviews

 (2)
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Bethan Jones

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Web
Dead
Anonymous user #827's avatar image No country

Anonymous user #827

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This software only displays one gene at a time.

It does not read GFF file format properly. I had to manually alter the features of the GFF file to make it work. Ex. I had to change "five_prime_UTR" to "utr", "CDS" to "exon", "three_prime_UTR" to "utr".

You cannot use any genomic positions greater than 5,000,000 or you get an error
Error: Can't use string ("5000000") as an ARRAY ref while "strict refs" in use at FancyGene/Errors.pm line 218, <fh00001Os_WRKY_genes2.gff3.txt> line 38.

Bug reporting does not work. I tried reporting the bug and I got the following error:
Not Found
The requested URL /~drambald/cgi-bin/fancygene/bugreport.pl was not found on this server.
Apache/2.2.22 (FreeBSD) PHP/5.4.3 proxy_html/3.1.2 mod_ssl/2.2.22 OpenSSL/0.9.8q DAV/2 Server at bio.ieo.eu Port 80