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Links tagged with 'fungi'

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AHMIITool Content

http://www.wdcm.org/AHMII/ahmii.html [open in a new window]

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Model Organisms > Microbes
Model Organisms > Other Organisms
Model Organisms > Yeast

Agent to Help Microbial Information Integration (AHMII) offers a search engine for particular strains present in culture collections and databases in bacteria, fungi, yeasts and cell lines.

links directory index: 0
TitlePublication YearGoogle Scholar Citation Count
AHMII: Agent to Help Microbial Information Integration.20030
NAR Web Server Issue 2003
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tagsbacteria cell line fungi microbiological techniques reproducibility of results systems integration yeasts

antiSMASHTool Content

http://antismash.secondarymetabolites.org [open in a new window]

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DNA > Annotations
Model Organisms > Microbes
Sequence Comparison > Multiple Sequence Alignments

The antibiotic and Secondary Metabolite Analysis Shell (antiSMASH) is a resource for identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.

links directory index: 19
TitlePublication YearGoogle Scholar Citation Count
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences201119
NAR Web Server Issue 2011
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tagsbacteria bacterial genes bacterial genome biosynthetic pathways fungal genes fungal genome fungi genomics molecular sequence annotation peptide synthases polyketide synthases substrate specificity

Argonne National Laboratory - Computational Biology DatabasesTool Content

http://www-unix.mcs.anl.gov/compbio/index.html [open in a new window]

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Protein > Networks & Interactions, Pathways and Enzymes

Provides several tools including WIT2, EMP, MPW, SENTRA and PatScan; other tools are also available.

links directory index: 833
TitlePublication YearGoogle Scholar Citation Count
Sentra, a database of signal transduction proteins200216
WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction2000369
MPW: the Metabolic Pathways Database1998127
Searching for patterns in genomic data1997221
The metabolic pathway collection from EMP: the enzymes and metabolic pathways database1996100
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tagsanimals bacteria biological transport chemotaxis conserved sequence enzymes eukaryota factual databases fungi genome humans metabolism methylation multigene family open reading frames phosphorylation prokaryotic cells protein databases protein kinases protein-serine-threonine kinases proteins sequence homology signal transduction systems integration tertiary protein structure

BioMart CentralDatabase Content

http://central.biomart.org/ [open in a new window]

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DNA > DNA and Genomic Analysis
Human Genome > Other Resources
Model Organisms > Databases
Protein > Proteomics

BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. The system also simplifies cross-database searches that might otherwise require several complicated steps.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
BioMart Central Portal: an open database network for the biological community20119
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tagsanimals bacteria biomedical research database management systems factual databases fungi genome humans international cooperation viruses

ITS2Tool Content

http://its2.bioapps.biozentrum.uni-wuerzburg.de/ [open in a new window]

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DNA > Phylogeny Reconstruction
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

The Internal Transcribed Spacer 2 Database (ITS2) includes a homology based RNA structure prediction algorithm which allows the detection and secondary structure prediction of ITS2 sequences. This resource also contains more than 25,000 pre-calculated secondary structures for currently known ITS2 sequences that can be searched and browsed via taxonomy.

links directory index: 276
TitlePublication YearGoogle Scholar Citation Count
The ITS2 Database III--sequences and structures for phylogeny201038
The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses200667
Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures200559
A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota2005112
NAR Web Server Issue 2006
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tagsanimals base sequence computational biology conserved sequence eukaryota fungal genome fungi genetic databases genetic markers genetic transcription invertebrates molecular evolution molecular models molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology phylogeny plant genome plants ribosomal rna ribosomal spacer dna rna sequence analysis sequence alignment tertiary protein structure

ITS2Database Content

http://its2.bioapps.biozentrum.uni-wuerzburg.de/cgi-bin/index.pl?search [open in a new window]

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DNA > Databases

The ITS2 Database holds information about sequence, structure and taxonomic classification of all internal transcribed spacer 2 (ITS2) in GenBank. ITS2 can now be searched with a modified BLAST considering both sequence and structure, enabling rapid taxon sampling. Novel sequences can be annotated using the HMM based approach and modelled according to multiple template structures. Sequences can be searched for known and newly identified motifs.

links directory index: 38
TitlePublication YearGoogle Scholar Citation Count
The ITS2 Database III--sequences and structures for phylogeny201038
NAR Database Issue 2010
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tagsbase sequence computational biology fungal genome fungi genetic databases molecular sequence data nucleic acid databases nucleic acid sequence homology plant genome plants ribosomal spacer dna tertiary protein structure

MIPSDatabase Content

http://www.helmholtz-muenchen.de/en/ibis [open in a new window]

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Model Organisms > General Resources
Model Organisms > Other Organisms
Model Organisms > Plants
Model Organisms > Yeast
Protein > Networks & Interactions, Pathways and Enzymes
Sequence Comparison > Comparative Genomics

Munich Information Centre for Protein Sequences projects include: fungal genome analysis, plant genome bioinformatics, structural genomics, proteomics and genome annotation. Projects and databases include: CYGD, MNCDB, NGFN, MPPI, SIMAP, QUIPOS, MATDB, MOsDB, SPUTNIK, and PEDANT.

links directory index: 703
TitlePublication YearGoogle Scholar Citation Count
MIPS: curated databases and comprehensive secondary data resources in 201020119
MIPS: analysis and annotation of proteins from whole genomes2004422
MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics200487
MOsDB: an integrated information resource for rice genomics200317
Sputnik: a database platform for comparative plant genomics200350
The PEDANT genome database2003118
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tagsanimals arabidopsis arabidopsis proteins biological models complementary dna computational biology data mining dna transposable elements expressed sequence tags fungi gene duplication genetic databases genome genomics humans information storage and retrieval internet metabolomics mice micrornas neoplasm genes nucleic acid databases nucleic acid sequence homology oryza sativa phenotype plant genes plant genome protein binding protein databases protein interaction mapping protein sequence analysis proteins proteomics saccharomyces cerevisiae proteins sequence homology software systems integration user-computer interface

OrthoDBDatabase Content

http://cegg.unige.ch/orthodb [open in a new window]

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Protein > Databases

OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across 44 vertebrates, 25 arthropods, and 46 fungi. OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups, and facilitate comprehensive orthology database querying.

links directory index: 18
TitlePublication YearGoogle Scholar Citation Count
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011201118
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsamino acid sequence homology animals arthropods drosophila melanogaster fungi genes genetic databases genomics mice molecular evolution molecular sequence annotation phylogeny proteins saccharomyces cerevisiae tertiary protein structure vertebrates

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