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To enable the scientific community to effectively use the GO vocabularies and annotations, a number of web-based tools have been developed by both members of the GOC and third parties to search, browse and view the GO hierarchy and annotations (Table 1).

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While these 53 GO annotations included a number of different biological processes, the two most common categories were cell metabolism (9 of 53 annotations; p-value range 8.18×10−5 to 0.04) and neuronal differentiation or function (another 9 of 53 annotations; p-value range 8.87×10−5 to 0.03).

Based on human genome annotations and a number of well-characterized RNA databases (see Materials and Methods), these small RNA sequences were annotated as known miRNA, degradation fragments of non-coding RNA (tRNA, rRNA, snRNA/snoRNA et al)., genomic repeat, mRNA or unclassified.

Our annotations of a number of previously unannotated Tetrahymena mitochondrial-encoded genes, plus the availability of proteomic and bioinformatic identification of nuclear-encoded Tetrahymena mitochondrial genes (Smith et al. 2007), indicates that the remainder of the unknown Tetrahymena ORFs are largely nonribosomal, in agreement with a previous study (Brunk et al. 2003).

They confirm near-saturation coverage of our data sets, and indicate that automatic pipelines lead to mis-annotation or lack of annotation for a number of genes.

A single TE insertion can appear as several pieces within the RepeatMasker annotation for a number of reasons.

Information retrieved from the domain annotation indicated a number of genes possessing the DUF (Domains with Unannotated Functions) and the UCP (UnCharacterized Protein) domains.

We were able to suggest new annotation for a number of positively predicted proteins.

The initial annotation gave a number of hypervariable sequences found within the C. jejuni genomic shotgun sequence [ 4].

In addition to the clustering analyses of genes in an unsupervised fashion and without annotation information, a number of supervised methods have been proposed for predicting gene functions.

In addition, we have improved the genome annotation for a number of gene families with roles in the detoxification of xenobiotic agents.

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