This track shows multiple alignments of 48 sequences to the Ebola virus reference strain KJ660347v2/Guinea_Gueckedou-C07_2014. The 48 sequences are composed of 46 Ebola virus sequences from five strains, and 2 Marburg 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 the tree topology from Gire et.al (2014):
(((((((((((((KJ660347v2 KJ660346v2) KJ660348v2) NC_002549v1) KC242793v1) KC242792v1) KC242794v1) ((KC242799v1 KC242796v1) (JQ352763v1 AY354458v1))) ((KC242791v1 AF272001v1) KC242801v1)) ((((((((KC242788v1 KC242787v1) KC242789v1) KC242786v1) KC242790v1) KC242785v1) KC242784v1) HQ613403v1) HQ613402v1)) (KC242800v1 (KC242783v2 (FJ968794v1 (EU338380v1 (JX477165v1 (FJ621583v1 FJ621584v1))))))) ((NC_014373v1 (KC545396v1 (KC545395v1 (KC545394v1 KC545393v1)))) NC_014372v1)) (((NC_004161v1 FJ621585v1) (AB050936v1 JX477166v1)) ((((KC545392v1 KC545391v1) KC545390v1) KC545389v1) (NC_006432v1 (JN638998v1 KC589025v1))))) (NC_024781v1 NC_001608v3))
(((((((((((((Guinea_Gueckedou-C07_2014 Guinea_Kissidougou-C15_2014) Guinea_Gueckedou-C05_2014) NC_002549v1_1976) 1Eko_1996) Gabon_1994) 2Nza_1996) ((13709Kikwit_1995 13625Kikwit_1995) (Kikwit_1995 Zaire_1995))) ((Bonduni_1977 Mayinga_1976) deRoover_1976)) ((((((((Luebo43_2007 Luebo23_2007) Luebo4_2007) Luebo1_2007) Luebo5_2007) Luebo0_2007) Luebo9_2007) M-M_2007) 034-KS_2008)) (Ilembe_2002 (Maleo_1979 (Boniface_1976 (Yambio_2004 (Reston09-A_2009 (Reston08-A_2008 Reston08-C_2008))))))) ((Bundibugyo_2007 (EboBund-14_2012 (EboBund-122_2012 (EboBund-120_2012 EboBund-112_2012)))) Cote_dIvoire_1994)) (((Pennsylvania_1990 Reston08-E_2008) (Reston_1996 Alice_TX_USA_MkCQ8167_1996)) (((EboSud-682_2012 EboSud-609_2012) EboSud-603_2012) EboSud-602_2012) (Gulu_2000 (Nakisamata_2011 EboSud-639_2012))))) (Marburg_KitumCave_Kenya_1987 Marburg_MtElgon_Musoke_Kenya_1980))Framing tables 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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