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Results: 4

1.
Figure 3

Figure 3. E. histolytica protein families.. From: New Assembly, Reannotation and Analysis of the Entamoeba histolytica Genome Reveal New Genomic Features and Protein Content Information.

A) Size distribution of protein families. B) Functional assignments in Singletons (proteins not assigned to families) versus Proteins within Families. Hypothetical: predicted hypothetical proteins; Non-hypothetical: predicted proteins with functional assignments; Expressed: predicted proteins with EST (expressed sequence tag) support.

Hernan A. Lorenzi, et al. PLoS Negl Trop Dis. 2010 June;4(6):e716.
2.
Figure 2

Figure 2. Structural annotation improvement in the new E. histolytica assembly.. From: New Assembly, Reannotation and Analysis of the Entamoeba histolytica Genome Reveal New Genomic Features and Protein Content Information.

Comparative analysis of Pfam HMM searches statistics between equivalent genes in the old and new annotation. Blue bars, genes that have better statistics/hits in the old annotation compared to the new annotation; orange bars, old and new annotation genes give exactly the same result; yellow bars, number of genes from the new annotation with better statistics/hits compared to their counterparts in the old annotation.

Hernan A. Lorenzi, et al. PLoS Negl Trop Dis. 2010 June;4(6):e716.
3.
Figure 4

Figure 4. Entamoeba histolytica segmental genome duplications.. From: New Assembly, Reannotation and Analysis of the Entamoeba histolytica Genome Reveal New Genomic Features and Protein Content Information.

A) D1-type duplications flanked by unique 2.3 kb inverted repeats (IR), B) D2-type duplications flanked by EhERE1/EhLINE2- derived 1.2 kb IRs, C) D3-type duplications usually associated to EhLINE1, but lacking IRs, and D) D4-type duplications present in the vicinity of TE elements, and lacking IRs. Inverted red arrows: IRs; purple boxes: open reading frames; blue boxes: repetitive elements; DS identifiers correspond to GenBank accession numbers for the corresponding scaffolds.

Hernan A. Lorenzi, et al. PLoS Negl Trop Dis. 2010 June;4(6):e716.
4.
Figure 1

Figure 1. Re-mapping strategy to transfer old annotation . From: New Assembly, Reannotation and Analysis of the Entamoeba histolytica Genome Reveal New Genomic Features and Protein Content Information.

A) Steps followed to achieve the full mapping of OGA (9,846 gene models) into the new E. histolytica assembly, resulting in NGA (8,201 gene models). B) Mapping of the OGA gene models fell into different categories: genes with perfect map to new assembly (same structure), genes that map to a location but have to be modified (different structure), genes that mapped to a repeat (discarded), genes smaller than 100 amino acids (discarded if they had no evidence), genes that fell within tandem duplications (discarded), and other smaller categories (pseudogenes, truncated genes).

Hernan A. Lorenzi, et al. PLoS Negl Trop Dis. 2010 June;4(6):e716.

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