MycoCosm portal: gearing up for 1000 fungal genomes
Citations
1,223 citations
Cites background from "MycoCosm portal: gearing up for 100..."
...Genome sequences are now available for several mycorrhizal fungi and are valuable for resolving long-standing issues about their Genome sequences and annotations can be assessed through the JGI MycoCosm portal (http://genome.jgi-psf.org/programs/fungi/index.jsf; Grigoriev et al., 2014)....
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799 citations
588 citations
Cites background from "MycoCosm portal: gearing up for 100..."
...Genome assemblies and annotations for the organisms used in this study are available via the JGI Genome Portal MycoCosm (http://jgi.doe. gov/fungi; see also Table S1)....
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...into MycoCosm (78), a Web-based fungal resource for comparative analysis....
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...Grigoriev IV, et al. (2014) MycoCosm portal: Gearing up for 1000 fungal genomes....
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...All genomes were annotated using the JGI Annotation Pipeline (77), which combines several gene prediction and annotation methods with transcriptomics data, and integrates the annotated genomes into MycoCosm (78), a Web-based fungal resource for comparative analysis....
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558 citations
Cites background from "MycoCosm portal: gearing up for 100..."
...Finally, availability of fungal genomes is also lacking compared to bacteria, though there are efforts underway to change this [49]....
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469 citations
Cites methods from "MycoCosm portal: gearing up for 100..."
...gz: archive containing three files with Pfam, SCOP, and PDB annotations, each formatted as tab-separated lists with nine columns: (1,2) identifiers for query and target, (3-5, 6-8) domain start and end-position and total sequence length for both UniProt and database sequence, (9) HHblits E-value....
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References
14,075 citations
11,453 citations
"MycoCosm portal: gearing up for 100..." refers methods in this paper
...SignalP (14) is used to detect the sequence motifs responsible for protein localization, TMHMM (15) identifies possible transmembrane domains and InterProScan (16) predicts functional domains from Pfam (17) and other databases....
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9,415 citations
"MycoCosm portal: gearing up for 100..." refers methods in this paper
...SignalP (14) is used to detect the sequence motifs responsible for protein localization, TMHMM (15) identifies possible transmembrane domains and InterProScan (16) predicts functional domains from Pfam (17) and other databases....
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8,370 citations
"MycoCosm portal: gearing up for 100..." refers methods in this paper
...SignalP (14) is used to detect the sequence motifs responsible for protein localization, TMHMM (15) identifies possible transmembrane domains and InterProScan (16) predicts functional domains from Pfam (17) and other databases....
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4,259 citations
"MycoCosm portal: gearing up for 100..." refers background in this paper
...Interpro, KEGG and Swiss-Prot hits are used to map gene ontology (GO) terms (21)....
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...gov), Swiss-Prot (18), KEGG (19) and KOG (20) databases additionally facilitate functional interpretation....
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...Protein alignments to the NCBI’s nonredundant (http://www.ncbi.nlm.nih.gov), Swiss-Prot (18), KEGG (19) and KOG (20) databases additionally facilitate functional interpretation....
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...Additionally, summaries listing numbers of genes by category in the GO, KEGG and KOG classifications are accessible from the portal menu, and can be compared with other selected genomes to explore gene family expansions and contractions across genomes....
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...Mycocosm therefore includes tools that integrate single genomes into a comparative context, such as the ability to visualize variation in gene counts in different GO, KEGG and KOG categories across a user-selected assortment of genomes....
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