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FUNGIpath specifications

Information


Unique identifier OMICS_05363
Name FUNGIpath
Restrictions to use None
Maintained No

Taxon


  • Plants and Fungi
    • Saccharomyces cerevisiae

Publication for FUNGIpath

FUNGIpath citations

 (6)
call_split

Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction

2017
Biotechnol Biofuels
PMCID: 5588705
PMID: 28912831
DOI: 10.1186/s13068-017-0897-7
call_split See protocol

[…] ter (using an 800 bp upstream region), and terminator (using a 200-bp downstream region).Functions of genes were predicted by similarity to orthologous genes when found in other fungal taxa using the FUNGIpath database (http://embg.igmors.u-psud.fr/fungipath/). If no orthologous gene function could be identified but a gene with a homology e-value superior to e-10 was identified, the product of thi […]

library_books

Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts

2015
Sci Rep
PMCID: 4479816
PMID: 26108467
DOI: 10.1038/srep11571

[…] Orthologs were first selected using blast with a P-value of 10−5 against proteomes of strains listed in . Single-copy G. candidum genes were verified using ORCAE and homology was verified using Fungipath. Sequences were concatenated and were aligned using MUSCLE v3.8 with default settings. Alignments were curated using GBlocks v0.91b. Species trees were reconstructed using PhyML v2.4.4 with […]

library_books

Kinetic transcriptome analysis reveals an essentially intact induction system in a cellulase hyper producer Trichoderma reesei strain

2014
Biotechnol Biofuels
PMCID: 4279801
PMID: 25550711
DOI: 10.1186/s13068-014-0173-z

[…] ase of genes that were either poorly or not yet annotated, orthologous genes in other fungal taxa (mainly Neurospora crassa, Saccharomyces cerevisiae and Aspergillus nidulans) were searched using the FUNGIpath database (http://embg.igmors.u-psud.fr/fungipath/) and the function predicted by similarity. Genes without orthologs were annotated with their domains either from the T. reesei genome websit […]

library_books

Maintenance of Sex Related Genes and the Co Occurrence of Both Mating Types in Verticillium dahliae

2014
PLoS One
PMCID: 4226480
PMID: 25383550
DOI: 10.1371/journal.pone.0112145

[…] mous (silent) substitutions in V. dahliae genes (relative to sexual fungi) were calculated through the SELECTON server , . All MAT genes used in this study were either identified directly through the FUNGIPath database, or were obtained through NCBI GenBank and verified as orthologs to either MAT1-1-1 or MAT1-2-1 using the ortholog search function in the FUNGIPath.Additionally, ortholog search res […]

library_books

A Network of HMG box Transcription Factors Regulates Sexual Cycle in the Fungus Podospora anserina

2013
PLoS Genet
PMCID: 3730723
PMID: 23935511
DOI: 10.1371/journal.pgen.1003642

[…] ger.ac.uk/ and http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml, respectively. N. crassa HMG-box genes were obtained from http://www.broadinstitute.org/annotation/genome/neurospora/MultiHome.html. FUNGIpath was used to identify systemically orthologous groups of genes (http://embg.igmors.u-psud.fr/fungipath/). Subcellular localization was predicted with PSORTII at http://psort.hgc.jp/form2.ht […]

call_split

The Transcriptional Response to Nonself in the Fungus Podospora anserina

2013
PMCID: 3689799
PMID: 23589521
DOI: 10.1534/g3.113.006262
call_split See protocol

[…] est. Secondary metabolism clusters were identified and analyzed with antismash at http://antismash.secondarymetabolites.org/ (). P. anserina and N. crassa orthologous gene pairs were identified using FUNGIpath (). Transposon sequence counting was restricted to the most frequent elements, the crapaud and discoglosse elements (). The list of genes encoding carbohydrate active enzymes was recovered a […]

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FUNGIpath institution(s)
Institut de Génétique et de Microbiologie, Université Paris-Sud 11, CNRS UMR 8621, Orsay, France

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