Comparison of protein coding gene content of yeasts and filamentous fungi

Mikko Arvas (Corresponding author), Teemu Kivioja, Alex Mitchell, Markku Saloheimo, Steve Oliver, Merja Penttilä

Research output: Contribution to conferenceOther conference contributionScientific

Abstract

The recent sequencing efforts have revealed that fungal genomes contain many genes with little or no homology to known genes (20% - 40% of CDS with no hits in Interpro, www.ebi.ac.uk/interpro/index.html). Comparisons to other fungal genomes can add power to the genomic analysis by providing the evolutionary context of genes. Our goal is to compare the protein coding gene contents of fungal genomes and relate the differences to the physiological differences between species and taxonomic groups. However, no single repository currently provides consistent gene annotations of all sequenced fungi. We have produced consistent Interpro annotations and Tribe-MCL (www.ebi.ac.uk/research/cgg/tribe/) clustering of protein coding sequences of 16 sequenced fungal genomes. Our computational system is based on BioPerl (bio.perl.org) scripts, BioSQL schema for storing the sequences and annotations in a relational database and GBrowse (www.gmod.org) genome browser for visualising genomes, genes and gene clusters. By combining these data sources and technology we can carry out comparative genome analysis, offer a local comparative genome browser for experimental biologists and profit from the efforts of BioPerl bioinformatics community.
Original languageEnglish
Publication statusPublished - 2005
EventEUROFUNGBASE Meeting - Sevilla, Spain
Duration: 16 Nov 200519 Nov 2005

Conference

ConferenceEUROFUNGBASE Meeting
CountrySpain
CitySevilla
Period16/11/0519/11/05

Fingerprint

Fungal Genome
Fungi
Yeasts
Genome
Genes
Proteins
Molecular Sequence Annotation
Information Storage and Retrieval
Multigene Family
Computational Biology
Cluster Analysis
Databases
Technology
Research

Cite this

Arvas, M., Kivioja, T., Mitchell, A., Saloheimo, M., Oliver, S., & Penttilä, M. (2005). Comparison of protein coding gene content of yeasts and filamentous fungi. EUROFUNGBASE Meeting, Sevilla, Spain.
Arvas, Mikko ; Kivioja, Teemu ; Mitchell, Alex ; Saloheimo, Markku ; Oliver, Steve ; Penttilä, Merja. / Comparison of protein coding gene content of yeasts and filamentous fungi. EUROFUNGBASE Meeting, Sevilla, Spain.
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abstract = "The recent sequencing efforts have revealed that fungal genomes contain many genes with little or no homology to known genes (20{\%} - 40{\%} of CDS with no hits in Interpro, www.ebi.ac.uk/interpro/index.html). Comparisons to other fungal genomes can add power to the genomic analysis by providing the evolutionary context of genes. Our goal is to compare the protein coding gene contents of fungal genomes and relate the differences to the physiological differences between species and taxonomic groups. However, no single repository currently provides consistent gene annotations of all sequenced fungi. We have produced consistent Interpro annotations and Tribe-MCL (www.ebi.ac.uk/research/cgg/tribe/) clustering of protein coding sequences of 16 sequenced fungal genomes. Our computational system is based on BioPerl (bio.perl.org) scripts, BioSQL schema for storing the sequences and annotations in a relational database and GBrowse (www.gmod.org) genome browser for visualising genomes, genes and gene clusters. By combining these data sources and technology we can carry out comparative genome analysis, offer a local comparative genome browser for experimental biologists and profit from the efforts of BioPerl bioinformatics community.",
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Arvas, M, Kivioja, T, Mitchell, A, Saloheimo, M, Oliver, S & Penttilä, M 2005, 'Comparison of protein coding gene content of yeasts and filamentous fungi', EUROFUNGBASE Meeting, Sevilla, Spain, 16/11/05 - 19/11/05.

Comparison of protein coding gene content of yeasts and filamentous fungi. / Arvas, Mikko (Corresponding author); Kivioja, Teemu; Mitchell, Alex; Saloheimo, Markku; Oliver, Steve; Penttilä, Merja.

2005. EUROFUNGBASE Meeting, Sevilla, Spain.

Research output: Contribution to conferenceOther conference contributionScientific

TY - CONF

T1 - Comparison of protein coding gene content of yeasts and filamentous fungi

AU - Arvas, Mikko

AU - Kivioja, Teemu

AU - Mitchell, Alex

AU - Saloheimo, Markku

AU - Oliver, Steve

AU - Penttilä, Merja

N1 - CA2: BEL2 BEL6 CA: BEL

PY - 2005

Y1 - 2005

N2 - The recent sequencing efforts have revealed that fungal genomes contain many genes with little or no homology to known genes (20% - 40% of CDS with no hits in Interpro, www.ebi.ac.uk/interpro/index.html). Comparisons to other fungal genomes can add power to the genomic analysis by providing the evolutionary context of genes. Our goal is to compare the protein coding gene contents of fungal genomes and relate the differences to the physiological differences between species and taxonomic groups. However, no single repository currently provides consistent gene annotations of all sequenced fungi. We have produced consistent Interpro annotations and Tribe-MCL (www.ebi.ac.uk/research/cgg/tribe/) clustering of protein coding sequences of 16 sequenced fungal genomes. Our computational system is based on BioPerl (bio.perl.org) scripts, BioSQL schema for storing the sequences and annotations in a relational database and GBrowse (www.gmod.org) genome browser for visualising genomes, genes and gene clusters. By combining these data sources and technology we can carry out comparative genome analysis, offer a local comparative genome browser for experimental biologists and profit from the efforts of BioPerl bioinformatics community.

AB - The recent sequencing efforts have revealed that fungal genomes contain many genes with little or no homology to known genes (20% - 40% of CDS with no hits in Interpro, www.ebi.ac.uk/interpro/index.html). Comparisons to other fungal genomes can add power to the genomic analysis by providing the evolutionary context of genes. Our goal is to compare the protein coding gene contents of fungal genomes and relate the differences to the physiological differences between species and taxonomic groups. However, no single repository currently provides consistent gene annotations of all sequenced fungi. We have produced consistent Interpro annotations and Tribe-MCL (www.ebi.ac.uk/research/cgg/tribe/) clustering of protein coding sequences of 16 sequenced fungal genomes. Our computational system is based on BioPerl (bio.perl.org) scripts, BioSQL schema for storing the sequences and annotations in a relational database and GBrowse (www.gmod.org) genome browser for visualising genomes, genes and gene clusters. By combining these data sources and technology we can carry out comparative genome analysis, offer a local comparative genome browser for experimental biologists and profit from the efforts of BioPerl bioinformatics community.

M3 - Other conference contribution

ER -

Arvas M, Kivioja T, Mitchell A, Saloheimo M, Oliver S, Penttilä M. Comparison of protein coding gene content of yeasts and filamentous fungi. 2005. EUROFUNGBASE Meeting, Sevilla, Spain.