This track shows multiple alignments of 160 virus sequences, composed of 158 sequences to the $Organism reference sequence G3683/KM034562.1 and two Marburg virus sequences. The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline.
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.
Pairwise alignments of each species to the $Organism 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.
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.
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 $Organism sequence at those alignment positions relative to the longest non-$Organism 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:
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=1Pairwise 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.
This track was created using the following programs:
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
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
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
Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468
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