160 Strains Track Settings
 
Multiz Alignment & Conservation (160 Virus Strains, Strain Names)   (All Comparative Genomics tracks)

Maximum display mode:       Reset to defaults
Select views (Help):
Multiz Alignments ▾       Basewise Conservation (phyloP) ▾       Element Conservation (phastCons) ▾       Conserved Elements ▾      
 
Multiz Alignments Configuration

Species selection:  + -

  Ebola 2014  + -

guinea_Kissidougou-C15_2014
guinea_Gueckedou-C07_2014
guinea_Gueckedou-C05_2014
eM095B_2014
eM095_2014
eM096_2014
eM098_2014
g3670v1_2014
g3676v1_2014
g3676v2_2014
g3677v1_2014
g3677v2_2014
g3679v1_2014
g3680v1_2014
g3682v1_2014
g3683v1_2014
g3687v1_2014
eM104_2014
eM106_2014
eM110_2014
eM111_2014
eM112_2014
eM113_2014
eM115_2014
eM119_2014
eM120_2014
eM121_2014
eM124v1_2014
eM124v2_2014
eM124v3_2014
eM124v4_2014
g3707_2014
g3713v2_2014
g3713v3_2014
g3713v4_2014
g3724_2014
g3729_2014
g3734v1_2014
g3735v1_2014
g3735v2_2014
g3750v1_2014
g3750v2_2014
g3750v3_2014
g3752_2014
g3758_2014
g3764_2014
g3765v2_2014
g3769v1_2014
g3769v2_2014
g3769v3_2014
g3769v4_2014
g3770v1_2014
g3770v2_2014
g3771_2014
g3782_2014
g3786_2014
g3787_2014
g3788_2014
g3789v1_2014
g3795_2014
g3796_2014
g3798_2014
g3799_2014
g3800_2014
g3805v1_2014
g3805v2_2014
g3807_2014
g3808_2014
g3809_2014
g3810v1_2014
g3810v2_2014
g3814_2014
g3816_2014
g3817_2014
g3818_2014
g3819_2014
g3820_2014
g3821_2014
g3822_2014
g3823_2014
g3825v1_2014
g3825v2_2014
g3826_2014
g3827_2014
g3829_2014
g3831_2014
g3834_2014
g3838_2014
g3840_2014
g3841_2014
g3845_2014
g3846_2014
g3848_2014
g3850_2014
g3851_2014
g3856v1_2014
g3856v3_2014
g3857_2014
nM042v1_2014
nM042v2_2014
nM042v3_2014

  DRC 2007  + -

ilembe_2002
034-KS_2008
m-M_2007
luebo9_2007
luebo0_2007
luebo1_2007
luebo23_2007
luebo43_2007
luebo4_2007
luebo5_2007
zaire_1995
kikwit_1995
13625Kikwit_1995
13709Kikwit_1995
gabon_1994
1Eko_1996
2Nza_1996
1Mbie_Gabon_1996
1Oba_Gabon_1996
1Ikot_Gabon_1996

  Zaire(DRC) 1976-7  + -

guineaPig_Mayinga_2007
mouse_Mayinga_2002
mayinga_2002
aF086833v2_1976
mayinga_1976
bonduni_1977
deRoover_1976
nC_002549v1_1976

  Bundibugyo 2007  + -

eboBund-112_2012
eboBund-120_2012
eboBund-122_2012
eboBund-14_2012
bundibugyo_Uganda_2007
bundibugyo_2007
cote_dIvoire_CIEBOV_1994
cote_dIvoire_1994

  Reston 1989-90  + -

reston_PA_1990
reston09-A_2009
pennsylvania_1990
reconstructReston_2008
reston08-A_2008
reston08-C_2008
reston_1996
alice_TX_USA_MkCQ8167_1996
reston08-E_2008

  Sudan 1976-9  + -

eboSud-602_2012
eboSud-603_2012
eboSud-609_2012
eboSud-682_2012
eboSud-639_2012
nakisamata_2011
boniface_1976
maleo_1979
yambio_2004
gulu_Uganda_2000
gulu_2000

  Marburg 1987  + -

marburg_KitumCave_Kenya_1987
marburg_MtElgon_Musoke_Kenya_1980

Multiple alignment base-level:
Display bases identical to reference as dots
Display chains between alignments

Codon Changes:
Display synonymous and non-synonymous changes in coding exons.

Codon Translation:
Default species to establish reading frame:
No codon translation
Use default species reading frames for translation
Use reading frames for species if available, otherwise no translation
Use reading frames for species if available, otherwise use default species
List subtracks: only selected/visible    all  
 
pack
 PhyloP  158 Ebola strains and 2 Marburg strains Basewise Conservation by PhyloP   Data format 
 
pack
 PhastCons  158 Ebola strains and 2 Marburg strains Basewise Conservation by PhastCons   Data format 
 
dense
 Cons. Elements  158 Ebola strains and 2 Marburg strains Conserved Elements   Data format 
 
pack
 Multiz Align  Multiz Genome Alignments of 158 Ebola strains and 2 Marburg strains   Data format 
Assembly: Ebola virus Sierra Leone 2014 (G3683/KM034562.1/eboVir3)

Downloads for data in this track are available:

Description

This track shows multiple alignments of 160 virus sequences, composed of 158 Ebola virus sequences and two Marburg virus sequences aligned to the Ebola virus reference sequence G3683/KM034562.1. It also includes measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package, for all 160 virus sequences. The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are also displayed in this track.

PhastCons (which has been used in previous Conservation tracks) is a hidden Markov model-based method that estimates the probability that each nucleotide belongs to a conserved element, based on the multiple alignment. It considers not just each individual alignment column, but also its flanking columns. By contrast, phyloP separately measures conservation at individual columns, ignoring the effects of their neighbors. As a consequence, the phyloP plots have a less smooth appearance than the phastCons plots, with more "texture" at individual sites. The two methods have different strengths and weaknesses. PhastCons is sensitive to "runs" of conserved sites, and is therefore effective for picking out conserved elements. PhyloP, on the other hand, is more appropriate for evaluating signatures of selection at particular nucleotides or classes of nucleotides (e.g., third codon positions, or first positions of miRNA target sites).

Another important difference is that phyloP can measure acceleration (faster evolution than expected under neutral drift) as well as conservation (slower than expected evolution). In the phyloP plots, sites predicted to be conserved are assigned positive scores (and shown in blue), while sites predicted to be fast-evolving are assigned negative scores (and shown in red). The absolute values of the scores represent -log p-values under a null hypothesis of neutral evolution. The phastCons scores, by contrast, represent probabilities of negative selection and range between 0 and 1.

Both phastCons and phyloP treat alignment gaps and unaligned nucleotides as missing data.

The data contained in the 160 Accessions and the 160 Strains tracks are the same. The only difference between these two tracks are the identifiers used to label the sequences. In the 160 Accessions track, the sequence is labeled using its NCBI Nucleotide accession number. In the 160 Strains track, we used a shortened version of the strain name from the NCBI Nucleotide entry to label each sequence, and when this was unavailable, we constructed our own using the DEFINITION, /country, and /collection_date lines from the NCBI record.

The mapping between sequence identifiers and strain names is provided via a text file on our download server. Additional meta information from Genbank is provided in a tab-separated file.

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 are 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

Pairwise alignments with the reference sequence were generated for each sequence using lastz version 1.03.52. Parameters used for each lastz alignment:

# hsp_threshold      = 2200
# gapped_threshold   = 4000 = L
# x_drop             = 910
# y_drop             = 3400 = Y
# gap_open_penalty   = 400
# gap_extend_penalty = 30
#        A    C    G    T
#   A   91  -90  -25 -100
#   C  -90  100 -100  -25
#   G  -25 -100  100  -90
#   T -100  -25  -90   91
# seed=1110100110010101111 w/transition
# step=1
Pairwise alignments were then linked into chains using a dynamic programming algorithm that finds maximally scoring chains of gapless subsections of the alignments organized in a kd-tree. Parameters used in the chaining (axtChain) step: -minScore=10 -linearGap=loose

High-scoring chains were then placed along the genome, with gaps filled by lower-scoring chains, to produce an alignment net.

The multiple alignment was constructed from the resulting best-in-genome pairwise alignments progressively aligned using multiz/autoMZ, following a simple binary tree phylogeny:

(((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((
(((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((
(KM034562v1 KJ660346v2) KJ660347v2) KJ660348v2) KM034554v1) KM034555v1) 
KM034557v1) KM034560v1) KM233039v1) KM233043v1) KM233045v1) KM233050v1) 
KM233051v1) KM233053v1) KM233056v1) KM233057v1) KM233063v1) KM233069v1) 
KM233070v1) KM233072v1) KM233089v1) KM233092v1) KM233096v1) KM233097v1) 
KM233098v1) KM233099v1) KM233103v1) KM233104v1) KM233109v1) KM233110v1) 
KM233113v1) AF086833v2) AF272001v1) AY142960v1) EU224440v2) KC242791v1) 
KC242792v1) KC242794v1) KC242796v1) KC242798v1) KC242799v1) KC242801v1) 
KM034551v1) KM034553v1) KM034556v1) KM034558v1) KM034559v1) KM034561v1) 
KM233035v1) KM233036v1) KM233037v1) KM233038v1) KM233040v1) KM233041v1) 
KM233042v1) KM233044v1) KM233046v1) KM233047v1) KM233048v1) KM233049v1) 
KM233052v1) KM233054v1) KM233055v1) KM233058v1) KM233059v1) KM233061v1) 
KM233062v1) KM233064v1) KM233065v1) KM233066v1) KM233067v1) KM233068v1) 
KM233071v1) KM233073v1) KM233074v1) KM233075v1) KM233076v1) KM233077v1) 
KM233078v1) KM233079v1) KM233080v1) KM233081v1) KM233082v1) KM233084v1) 
KM233085v1) KM233086v1) KM233087v1) KM233088v1) KM233093v1) KM233094v1) 
KM233095v1) KM233100v1) KM233101v1) KM233102v1) KM233105v1) KM233106v1) 
KM233107v1) KM233108v1) KM233111v1) KM233112v1) KM233114v1) KM233115v1) 
KM233116v1) KM233091v1) NC_002549v1) KM034552v1) KM233060v1) KM233083v1) 
KM233090v1) KM233117v1) KM233118v1) AY354458v1) KC242784v1) KC242785v1) 
KC242786v1) KC242787v1) KC242788v1) KC242789v1) KC242790v1) KC242793v1) 
KC242795v1) KC242797v1) KC242800v1) AF499101v1) JQ352763v1) HQ613402v1) 
HQ613403v1) KM034549v1) KM034550v1) KM034563v1) FJ217162v1) NC_014372v1) 
FJ217161v1) NC_014373v1) KC545395v1) KC545394v1) KC545393v1) KC545396v1) 
FJ621585v1) FJ621584v1) JX477166v1) AY769362v1) AB050936v1) EU338380v1) 
KC242783v2) JX477165v1) AF522874v1) NC_004161v1) FJ621583v1) KC589025v1) 
FJ968794v1) AY729654v1) NC_006432v1) KC545389v1) KC545390v1) KC545391v1) 
KC545392v1) JN638998v1) NC_024781v1) NC_001608v3)
(((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((
(((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((
(G3686v1_2014 Guinea_Kissidougou-C15_2014) Guinea_Gueckedou-C07_2014) 
Guinea_Gueckedou-C05_2014) G3676v1_2014) G3676v2_2014) G3677v2_2014) 
G3682v1_2014) EM112_2014) EM120_2014) EM124v1_2014) G3713v2_2014) G3713v3_2014) 
G3724_2014) G3735v1_2014) G3735v2_2014) G3764_2014) G3770v1_2014) G3770v2_2014) 
G3782_2014) G3814_2014) G3818_2014) G3822_2014) G3823_2014) G3825v1_2014) 
G3825v2_2014) G3831_2014) G3834_2014) G3846_2014) G3848_2014) G3856v1_2014) 
AF086833v2_1976) Mayinga_1976) Mayinga_2002) GuineaPig_Mayinga_2007) 
Bonduni_1977) Gabon_1994) 2Nza_1996) 13625Kikwit_1995) 1Ikot_Gabon_1996) 
13709Kikwit_1995) deRoover_1976) EM096_2014) G3670v1_2014) G3677v1_2014) 
G3679v1_2014) G3680v1_2014) G3683v1_2014) EM104_2014) EM106_2014) EM110_2014) 
EM111_2014) EM113_2014) EM115_2014) EM119_2014) EM121_2014) EM124v2_2014) 
EM124v3_2014) EM124v4_2014) G3707_2014) G3713v4_2014) G3729_2014) G3734v1_2014) 
G3750v1_2014) G3750v2_2014) G3752_2014) G3758_2014) G3765v2_2014) G3769v1_2014) 
G3769v2_2014) G3769v3_2014) G3769v4_2014) G3771_2014) G3786_2014) G3787_2014) 
G3788_2014) G3789v1_2014) G3795_2014) G3796_2014) G3798_2014) G3799_2014) 
G3800_2014) G3805v1_2014) G3807_2014) G3808_2014) G3809_2014) G3810v1_2014) 
G3810v2_2014) G3819_2014) G3820_2014) G3821_2014) G3826_2014) G3827_2014) 
G3829_2014) G3838_2014) G3840_2014) G3841_2014) G3845_2014) G3850_2014) 
G3851_2014) G3856v3_2014) G3857_2014) NM042v1_2014) G3817_2014) 
NC_002549v1_1976) EM098_2014) G3750v3_2014) G3805v2_2014) G3816_2014) 
NM042v2_2014) NM042v3_2014) Zaire_1995) Luebo9_2007) Luebo0_2007) Luebo1_2007) 
Luebo23_2007) Luebo43_2007) Luebo4_2007) Luebo5_2007) 1Eko_1996) 
1Mbie_Gabon_1996) 1Oba_Gabon_1996) Ilembe_2002) Mouse_Mayinga_2002) 
Kikwit_1995) 034-KS_2008) M-M_2007) EM095B_2014) EM095_2014) G3687v1_2014) 
Cote_dIvoire_CIEBOV_1994) Cote_dIvoire_1994) Bundibugyo_Uganda_2007) 
Bundibugyo_2007) EboBund-122_2012) EboBund-120_2012) EboBund-112_2012) 
EboBund-14_2012) Reston08-E_2008) Reston08-C_2008) Alice_TX_USA_MkCQ8167_1996) 
reconstructReston_2008) Reston_1996) Yambio_2004) Maleo_1979) Reston09-A_2009) 
Reston_PA_1990) Pennsylvania_1990) Reston08-A_2008) EboSud-639_2012) 
Boniface_1976) Gulu_Uganda_2000) Gulu_2000) EboSud-602_2012) EboSud-603_2012) 
EboSud-609_2012) EboSud-682_2012) Nakisamata_2011) 
Marburg_KitumCave_Kenya_1987) Marburg_MtElgon_Musoke_Kenya_1980)
Framing tables from the genes were constructed to enable visualization of codons in the multiple alignment display.

Phylogenetic Tree Model

Both phastCons and phyloP are phylogenetic methods that rely on a tree model containing the tree topology, branch lengths representing evolutionary distance at neutrally evolving sites, the background distribution of nucleotides, and a substitution rate matrix. The all-species tree model for this track was generated using the phyloFit program from the PHAST package (REV model, EM algorithm, medium precision) using multiple alignments of 4-fold degenerate sites extracted from the 160-way alignment (msa_view). The 4d sites were derived from the NCBI gene set, filtered to select single-coverage long transcripts.

This same tree model was used in the phyloP calculations; however, the background frequencies were modified to maintain reversibility. The resulting tree model: all species.

PhastCons Conservation

The phastCons program computes conservation scores based on a phylo-HMM, a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for conserved regions and a state for non-conserved regions. The value plotted at each site is the posterior probability that the corresponding alignment column was "generated" by the conserved state of the phylo-HMM. These scores reflect the phylogeny (including branch lengths) of the species in question, a continuous-time Markov model of the nucleotide substitution process, and a tendency for conservation levels to be autocorrelated along the genome (i.e., to be similar at adjacent sites). The general reversible (REV) substitution model was used. Unlike many conservation-scoring programs, phastCons does not rely on a sliding window of fixed size; therefore, short highly-conserved regions and long moderately conserved regions can both obtain high scores. More information about phastCons can be found in Siepel et al, 2005.

The phastCons parameters used were: expected-length=45, target-coverage=0.3, rho=0.3.

PhyloP Conservation

The phyloP program supports several different methods for computing p-values of conservation or acceleration, for individual nucleotides or larger elements (http://compgen.cshl.edu/phast/). Here it was used to produce separate scores at each base (--wig-scores option), considering all branches of the phylogeny rather than a particular subtree or lineage (i.e., the --subtree option was not used). The scores were computed by performing a likelihood ratio test at each alignment column (--method LRT), and scores for both conservation and acceleration were produced (--mode CONACC).

Conserved Elements

The conserved elements were predicted by running phastCons with the --most-conserved option. The predicted elements are segments of the alignment that are likely to have been "generated" by the conserved state of the phylo-HMM. Each element is assigned a log-odds score equal to its log probability under the conserved model minus its log probability under the non-conserved model. The "score" field associated with this track contains transformed log-odds scores, taking values between 0 and 1000. (The scores are transformed using a monotonic function of the form a * log(x) + b.) The raw log odds scores are retained in the "name" field and can be seen on the details page or in the browser when the track's display mode is set to "pack" or "full".

Credits

This track was created using the following programs:

  • Alignment tools: lastz (formerly blastz) and multiz by Minmei Hou, Scott Schwartz, Robert Harris, and Webb Miller of the Penn State Bioinformatics Group
  • Conservation scoring: phastCons, phyloP, phyloFit, tree_doctor, msa_view and other programs in PHAST by Adam Siepel at Cold Spring Harbor Laboratory (original development done at the Haussler lab at UCSC).
  • Chaining and Netting: axtChain, chainNet by Jim Kent at UCSC
  • MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC
  • Tree image generator: phyloPng by Galt Barber, UCSC
  • Conservation track display: Kate Rosenbloom, Hiram Clawson (wiggle display), and Brian Raney (gap annotation and codon framing) at UCSC

References

Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G et al. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 2014 Sep 12;345(6202):1369-72. PMID: 25214632; Supplemental Materials and Methods

Phylo-HMMs, phastCons, and phyloP:

Felsenstein J, Churchill GA. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol. 1996 Jan;13(1):93-104. PMID: 8583911

Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21. PMID: 19858363; PMC: PMC2798823

Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. PMID: 16024819; PMC: PMC1182216

Siepel A, Haussler D. Phylogenetic Hidden Markov Models. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351.

Yang Z. A space-time process model for the evolution of DNA sequences. Genetics. 1995 Feb;139(2):993-1005. PMID: 7713447; PMC: PMC1206396

Chain/Net:

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784

Multiz:

Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 Apr;14(4):708-15. PMID: 15060014; PMC: PMC383317

Lastz (formerly Blastz):

Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468

Harris RS. Improved pairwise alignment of genomic DNA. Ph.D. Thesis. Pennsylvania State University, USA. 2007.

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961