FancyGene protocols

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description
FancyGene computational protocol

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

 (2)
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 [32] was used to present gene structures on the genome. alignments of amino-acid sequences were performed using clustalw [33]. prediction of transmembrane domains was performed using […]

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 [22]. sequence alignments were performed using […]

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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Web
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