Description

This track shows the alignments of recently sequenced Ebola samples to the Ebola virus reference sequence G3683/KM034562.1.

Display Conventions and Configuration

Pairwise alignments of each species to the Ebola virus genome are displayed as a series of colored blocks indicating the functional effect of polymorphisms (in pack mode), or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, percent identity of the whole alignments is shown in grayscale using darker values to indicate higher levels of identity.

In pack mode, regions that align with 100% identity are not shown. When there is not 100% percent identity, blocks of four colors are drawn.

• Red blocks are drawn when a polymorphism in a coding region results in a change in the amino acid that is generated.
• Green blocks are drawn when a polymorphism in a coding region results in no change to the amino acid that is generated.
• Blue blocks are drawn when a polymorphism is outside a coding region.
• Pale yellow blocks are drawn when there is no aligning bases to that region in the reference genome.

Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. Configuration buttons are available to select all of the species (Set all), deselect all of the species (Clear all), or use the default settings (Set defaults).

To view detailed information about the alignments at a specific position, zoom the display in to 30,000 or fewer bases, then click on the alignment.

Base Level

When zoomed-in to the base-level display, the track shows the base composition of each alignment. The numbers and symbols on the Gaps line indicate the lengths of gaps in the Ebola virus sequence at those alignment positions relative to the longest non-Ebola virus sequence. If there is sufficient space in the display, the size of the gap is shown. If the space is insufficient and the gap size is a multiple of 3, a "*" is displayed; other gap sizes are indicated by "+".

Codon translation is available in base-level display mode if the displayed region is identified as a coding segment. To display this annotation, select the species for translation from the pull-down menu in the Codon Translation configuration section at the top of the page. Then, select one of the following modes:

• No codon translation: The gene annotation is not used; the bases are displayed without translation.
• Use default species reading frames for translation: The annotations from the genome displayed in the Default species to establish reading frame pull-down menu are used to translate all the aligned species present in the alignment.
• Use reading frames for species if available, otherwise no translation: Codon translation is performed only for those species where the region is annotated as protein coding.
• Use reading frames for species if available, otherwise use default species: Codon translation is done on those species that are annotated as being protein coding over the aligned region using species-specific annotation; the remaining species are translated using the default species annotation.

Methods

Ebola sequences are found NCBI Nucleotide with the search term: (ebola[title] or ebolavirus[title]) and genome

The sequences are aligned to the reference sequence with an ordinary Smith-Waterman alignment command faAlign from the 'kent' source utilities.

Source information