This track shows multiple alignments to the $organism/NC_002549.1 reference strain, 160 virus sequences, composed of 158 ebola virus sequences 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.
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:
((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((( ((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((( (NC_002549v1 AF086833v2) AY142960v1) KC242791v1) KC242801v1) AF272001v1) AF499101v1) EU224440v2) KC242799v1) KC242796v1) AY354458v1) JQ352763v1) KC242792v1) KC242793v1) KC242795v1) KC242797v1) KC242794v1) KC242798v1) KC242786v1) KC242787v1) KC242789v1) KC242784v1) KC242785v1) KC242790v1) KC242788v1) KC242800v1) HQ613403v1) HQ613402v1) KJ660347v2) KJ660346v2) KJ660348v2) KM034562v1) KM034555v1) KM034557v1) KM034554v1) KM233056v1) KM233113v1) KM233070v1) KM233053v1) KM233063v1) KM233050v1) KM233069v1) KM233109v1) KM233110v1) KM233057v1) KM034560v1) KM233097v1) KM233039v1) KM233096v1) KM233099v1) KM233072v1) KM233054v1) KM233051v1) KM233098v1) KM233103v1) KM233049v1) KM233080v1) KM233106v1) KM233092v1) KM233102v1) KM233052v1) KM233062v1) KM233114v1) KM034556v1) KM034559v1) KM233075v1) KM233100v1) KM034551v1) KM233081v1) KM233094v1) KM233116v1) KM034553v1) KM233065v1) KM233068v1) KM233084v1) KM233040v1) KM233047v1) KM233112v1) KM233104v1) KM233045v1) KM233088v1) KM034558v1) KM034561v1) KM233105v1) KM233037v1) KM233108v1) KM233043v1) KM233089v1) KM233073v1) KM233078v1) KM233038v1) KM233044v1) KM233035v1) KM233042v1) KM233067v1) KM233071v1) KM233077v1) KM034550v1) KM233061v1) KM233074v1) KM233041v1) KM233085v1) KM233091v1) KM233055v1) KM233093v1) KM233107v1) KM233066v1) KM233101v1) KM233036v1) KM233079v1) KM233046v1) KM233095v1) KM233087v1) KM233058v1) KM233115v1) KM233086v1) KM233048v1) KM034549v1) KM233076v1) KM233082v1) KM233064v1) KM233090v1) KM233059v1) KM233083v1) KM034552v1) KM233111v1) KM233060v1) KM233117v1) KM233118v1) KM034563v1) AF522874v1) NC_004161v1) AY769362v1) FJ621583v1) JX477166v1) JX477165v1) AB050936v1) FJ621585v1) FJ621584v1) JN638998v1) AY729654v1) NC_006432v1) KC545390v1) KC545391v1) KC545389v1) KC545392v1) KC589025v1) KC242783v2) FJ217161v1) NC_014373v1) KC545394v1) KC545395v1) KC545393v1) KC545396v1) FJ217162v1) NC_014372v1) EU338380v1) FJ968794v1) NC_024781v1) NC_001608v3)
((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((( ((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((( (NC_002549v1_1976 AF086833v2_1976) Mayinga_2002) Bonduni_1977) deRoover_1976) Mayinga_1976) Mouse_Mayinga_2002) GuineaPig_Mayinga_2007) 13709Kikwit_1995) 13625Kikwit_1995) Zaire_1995) Kikwit_1995) Gabon_1994) 1Eko_1996) 1Mbie_Gabon_1996) 1Oba_Gabon_1996) 2Nza_1996) 1Ikot_Gabon_1996) Luebo1_2007) Luebo23_2007) Luebo4_2007) Luebo9_2007) Luebo0_2007) Luebo5_2007) Luebo43_2007) Ilembe_2002) M-M_2007) 034-KS_2008) Guinea_Gueckedou-C07_2014) Guinea_Kissidougou-C15_2014) Guinea_Gueckedou-C05_2014) G3686v1_2014) G3676v2_2014) G3677v2_2014) G3676v1_2014) G3735v1_2014) G3856v1_2014) G3770v2_2014) G3724_2014) G3764_2014) G3713v2_2014) G3770v1_2014) G3846_2014) G3848_2014) G3735v2_2014) G3682v1_2014) G3823_2014) EM112_2014) G3822_2014) G3825v2_2014) G3782_2014) G3729_2014) G3713v3_2014) G3825v1_2014) G3831_2014) G3707_2014) G3799_2014) G3840_2014) G3818_2014) G3829_2014) G3713v4_2014) G3758_2014) G3856v3_2014) G3677v1_2014) G3680v1_2014) G3788_2014) G3826_2014) EM096_2014) G3800_2014) G3820_2014) NM042v1_2014) G3670v1_2014) G3769v1_2014) G3769v4_2014) G3807_2014) EM113_2014) EM124v3_2014) G3851_2014) G3834_2014) EM124v1_2014) G3810v2_2014) G3679v1_2014) G3683v1_2014) G3838_2014) EM110_2014) G3845_2014) EM120_2014) G3814_2014) G3786_2014) G3796_2014) EM111_2014) EM121_2014) EM104_2014) EM119_2014) G3769v3_2014) G3771_2014) G3795_2014) EM095_2014) G3752_2014) G3787_2014) EM115_2014) G3808_2014) G3817_2014) G3734v1_2014) G3819_2014) G3841_2014) G3769v2_2014) G3827_2014) EM106_2014) G3798_2014) EM124v2_2014) G3821_2014) G3810v1_2014) G3750v1_2014) G3857_2014) G3809_2014) EM124v4_2014) EM095B_2014) G3789v1_2014) G3805v1_2014) G3765v2_2014) G3816_2014) G3750v2_2014) G3805v2_2014) EM098_2014) G3850_2014) G3750v3_2014) NM042v2_2014) NM042v3_2014) G3687v1_2014) Reston_PA_1990) Pennsylvania_1990) reconstructReston_2008) Reston08-A_2008) Alice_TX_USA_MkCQ8167_1996) Reston09-A_2009) Reston_1996) Reston08-E_2008) Reston08-C_2008) Nakisamata_2011) Gulu_Uganda_2000) Gulu_2000) EboSud-603_2012) EboSud-609_2012) EboSud-602_2012) EboSud-682_2012) EboSud-639_2012) Maleo_1979) Bundibugyo_Uganda_2007) Bundibugyo_2007) EboBund-120_2012) EboBund-122_2012) EboBund-112_2012) EboBund-14_2012) Cote_dIvoire_CIEBOV_1994) Cote_dIvoire_1994) Yambio_2004) Boniface_1976) 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:
Stephen K. Gire, Augustine Goba, Kristian G. Andersen, ... Robert F. Garry, S. Humarr Khan, and Pardis C. Sabeti
Genomic surveillance elucidates Ebola virus origin
and transmission during the 2014 outbreak
Science 12 September 2014: 345 (6202), 1369-1372.
Published online 28 August 2014 [DOI:10.1126/science.1259657]
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