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Noncoding neutral variations are excluded because in most genes they outnumber coding variations and (1) are not the main interest of the database user, (2) locate in regions that are not included in standard exon-based mutation screening strategies, and (3) are rarely documented in detail in literature reports, the major resource of the database content.
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It is in the interest of the databases wishing to employ biocuration procedures to ensure best value for the investment made by funding bodies by ensuring that they work with existing resources available in the community, rather than 'reinventing the wheel' by redundantly developing multiple curation tools to annotate the same datasets.
One reason is that there are mutations in the papers that are not of interest to the databases, e.g. the scope of COSMIC is somatic mutations only while InSiGHT focuses on germline mutations in only four genes.
Thanks to this consolidation process, iRefWeb affords a global view of the consolidated data, and enables the exploration of the known interaction partners for a protein of interest, regardless of the database(s) that contain the original information.
There are mutations that are extracted by the mutation tools that do not appear in the curated databases, as found by Schench et al. This is because these mutations are not of the interest to the databases.
The proposed chemical identities are tentative, and in upcoming years, we anticipate to confirm the identities of key metabolites of interest in the database through the use of chemical standards.
In this study, the rough PPANs are constructed at first based on the selected proteins of interest and the database information of protein-protein interactions.
The fastest way to construct the network is to use formatdb to create a custom BLAST database of a sequence set of interest, search the database with each individual sequence in the set using blastall, and treat hits to each sequence better than a threshold E-value as edges.
While checking that out, note the POI (Points Of Interest) that the database shows you.
A tutorial for the database is available in the 'Help' page, including searching genes of interest, using the database to obtain reprogramming protocols and downloading the results for further analysis.
Beside the evolutionary interest of a database obtained from a member of the Chondrostean, certainly applied genetics studies on sturgeons will benefit from this resource.
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