Limits...
mycoCLAP, the database for characterized lignocellulose-active proteins of fungal origin: resource and text mining curation support.

Strasser K, McDonnell E, Nyaga C, Wu M, Wu S, Almeida H, Meurs MJ, Kosseim L, Powlowski J, Butler G, Tsang A - Database (Oxford) (2015)

Bottom Line: Fungi are prolific producers of these enzymes, spurring fungal genome sequencing efforts to identify and catalogue the genes that encode them.First implemented in 2011, and updated as described here, mycoCLAP is capable of ranking search results according to closest biochemically characterized homologues: this improves the quality of the annotation, and significantly decreases the time required to annotate novel sequences.The database is freely available to the scientific community, as are the open source applications based on natural language processing developed to support the manual curation of mycoCLAP.

View Article: PubMed Central - PubMed

Affiliation: Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA.

Show MeSH
Filtered view in mycoCLAP.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4352688&req=5

bav008-F5: Filtered view in mycoCLAP.

Mentions: By default, the search-results page lists all matching entries and displays the following fields: mycoCLAP Entry Name, Source Species, Enzyme Name, CAZy Family, Host used for recombinant expression, Substrate(s) and Assay(s) used to measure enzyme activity, Specific Activity in international units, pH and Temperature Optima, EC number, GenBank Protein ID, UniProt ID, literature PubMed ID and Date when the entry was last modified. In the tabular view, users can refine a search by clicking on any column header in the data table, moving the mouse to the empty field next to ‘Filters’ in the drop-down menu, and typing in the search term as shown in Fig. 5.Figure 5.


mycoCLAP, the database for characterized lignocellulose-active proteins of fungal origin: resource and text mining curation support.

Strasser K, McDonnell E, Nyaga C, Wu M, Wu S, Almeida H, Meurs MJ, Kosseim L, Powlowski J, Butler G, Tsang A - Database (Oxford) (2015)

Filtered view in mycoCLAP.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4352688&req=5

bav008-F5: Filtered view in mycoCLAP.
Mentions: By default, the search-results page lists all matching entries and displays the following fields: mycoCLAP Entry Name, Source Species, Enzyme Name, CAZy Family, Host used for recombinant expression, Substrate(s) and Assay(s) used to measure enzyme activity, Specific Activity in international units, pH and Temperature Optima, EC number, GenBank Protein ID, UniProt ID, literature PubMed ID and Date when the entry was last modified. In the tabular view, users can refine a search by clicking on any column header in the data table, moving the mouse to the empty field next to ‘Filters’ in the drop-down menu, and typing in the search term as shown in Fig. 5.Figure 5.

Bottom Line: Fungi are prolific producers of these enzymes, spurring fungal genome sequencing efforts to identify and catalogue the genes that encode them.First implemented in 2011, and updated as described here, mycoCLAP is capable of ranking search results according to closest biochemically characterized homologues: this improves the quality of the annotation, and significantly decreases the time required to annotate novel sequences.The database is freely available to the scientific community, as are the open source applications based on natural language processing developed to support the manual curation of mycoCLAP.

View Article: PubMed Central - PubMed

Affiliation: Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA.

Show MeSH