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Sequences not retrieved by our method but labeled as sHSP with one of the four annotations above were too small (50 residues or less) or defined as fragment (with a potentially incomplete ACD pattern).
Enrichment of terms and "Fisher's Exact" P-values were calculated as for GO annotations above against a background of all InterPro annotated genes in the UCSC Known Genes database.
Unless otherwise denoted, only domain annotations above the domain-specific gathering threshold provided by Pfam were considered.
In both versions ('all' and 'filtered' versions) of AcypiCyc and TricaCyc, the information about the annotation method and the CycADS extraction score for each EC and GO annotation can be found in the gene page as shown in Figure 2, while in the metabolism reconstruction only the EC and GO annotations above the chosen cutoff are taken into account.
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KEGG pathway and GO annotations described above were used to compute functional enrichment scores for all switch-like genes.
Metabolic pathways, implicated the intracellular metabolic pathways control immune tolerance and regulation of stem cell behaviour and life span, showed the highest number of transcripts here and corresponded to the results of GO annotation described above and published transcriptome report.
The annotation of the β-keratin genes is based upon our annotation (above the figure) and phylogenetic analyses (below the figure).
Although the assembly and annotation above described indicate the existence of large duplicated genomic regions in the genome of the ISA1307 strain, only two or three of the 13 chromosomal bands obtained in the PFGE gel seem to be duplicated (Fig. 1; see above).
This shows that the method is able to recover novel hits from both well-studied and rare domains, offering a similar sensitivity to alternative HMM building approaches [ 22] and extending the depth of annotation above that of the standard Pfam approach.
Each of these datasets were then annotated for overlap with the same annotations listed above.
(This, and other factoids Matthews should have had at the ready, are included in annotations of the above video).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com