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Cufflinks was run with the default parameters without supplying any annotation file.
Agilent supplies an annotation file for the array.
For example, TopHat/Cufflinks supports a mode that allows users to specify the transcriptome by supplying an annotation database (a GTF file).
Existing verification systems usually rely on users to supply annotations to guide the verification, which can be cumbersome and error-prone by hand and can significantly restrict the usability of the verification system.
The entries supply annotations of the ubiquitin-conjugated and the exact positions of the ubiquitin-conjugation sites.
Primary sources are those that are used to derive main disease names; some of them also supply annotations (15 sources).
For each annotated genomic component, we supplied detailed annotations and cross-links to publicly available databases.
Cufflinks (v2.1.1) was used for transcript assembly with supplied genome annotations [ 30].
If this option is enabled (disabled by default), our current algorithm adds novel exon-exon junctions detected from the RNA-seq data to the supplied transcript annotations.
Since 2010, UniProt-GOA has supplied GO annotations in a Gene Product Association Data GPADD) file format, which allows inclusion of ECO terms.
The RAVEN toolbox [ 65] allows for the curation of a reconstruction from models of related species using homologs identified through BLAST bidirectional best hits, and additional unique functions supplied through annotations taken from KEGG Orthology [ 26].
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