97805fb2ceb73357aa78aa94107148dc355d4e1c mspeir Tue Sep 22 08:36:22 2026 -0700 Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/ebola/resEbo1/cons160way.html src/hg/makeDb/trackDb/ebola/resEbo1/cons160way.html index 4cfc30821e4..aa85aaade12 100644 --- src/hg/makeDb/trackDb/ebola/resEbo1/cons160way.html +++ src/hg/makeDb/trackDb/ebola/resEbo1/cons160way.html @@ -1,204 +1,216 @@ <H2>Description</H2> <P> 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/<A HREF="http://www.bx.psu.edu/miller_lab/" TARGET=_blank>Penn State Bioinformatics</A> comparative genomics alignment pipeline. </P> <H2>Methods</H2> <P> Pairwise alignments with the reference sequence were generated for each sequence using lastz version 1.03.52. Parameters used for each lastz alignment: <pre> # 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 </pre> 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 </P> <P> High-scoring chains were then placed along the genome, with gaps filled by lower-scoring chains, to produce an alignment net. </P> <P> The multiple alignment was constructed from the resulting best-in-genome pairwise alignments progressively aligned using multiz/autoMZ, following a simple binary tree phylogeny: <pre> ((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((( ((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((( (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) </pre> <pre> ((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((( ((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((( (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) </pre> Framing tables from the genes were constructed to enable visualization of codons in the multiple alignment display.</P> +<h2>Data Access</h2> +<p> +The alignments and the conservation scores can be retrieved for a single region or for a list of +regions with the <a +href="hgTables?db=resEbo1&hgta_group=compGeno&hgta_track=cons160way">Table Browser</a>, +which returns the alignments in MAF format and the scores as wiggle data. The conservation +scores, though not the alignments, can also be joined with other annotations in the <a +href="hgIntegrator?db=resEbo1">Data Integrator</a>. For automated access, our <a +href="../goldenPath/help/api.html">REST API</a> serves the alignment and conservation tracks +individually, by name. +</p> + <H2>Credits</H2> <P> This track was created using the following programs: <UL> <LI> Alignment tools: blastz and multiz by Minmei Hou, Scott Schwartz and Webb Miller of the <A HREF="http://www.bx.psu.edu/miller_lab/" TARGET=_blank>Penn State Bioinformatics Group</A> <LI> Chaining and Netting: axtChain, chainNet by Jim Kent at UCSC <LI> Conservation scoring: phastCons, phyloP, phyloFit, tree_doctor, msa_view and other programs in PHAST by <A HREF="https://siepellab.labsites.cshl.edu/" TARGET=_blank>Adam Siepel</A> at Cold Spring Harbor Laboratory (original development done at the Haussler lab at UCSC). <LI> MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC <LI> Tree image generator: phyloPng by Galt Barber, UCSC <LI> Conservation track display: Kate Rosenbloom, Hiram Clawson (wiggle display), and Brian Raney (gap annotation and codon framing) at UCSC </UL> </P> <h2>References</h2> <h3>Phylo-HMMs, phastCons, and phyloP:</h3> <p> Stephen K. Gire, Augustine Goba, Kristian G. Andersen, ... Robert F. Garry, S. Humarr Khan, and Pardis C. Sabeti <a href="http://www.sciencemag.org/content/345/6202/1369.abstract" target="blank">Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak</a> <em>Science</em> 12 September 2014: 345 (6202), 1369-1372.<br> Published online 28 August 2014 [DOI:10.1126/science.1259657] </p> <p> Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. <a href="http://genome.cshlp.org/content/20/1/110.long" target="_blank"> Detection of nonneutral substitution rates on mammalian phylogenies</a>. <em>Genome Res</em>. 2010 Jan;20(1):110-21. </p> <p> Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, <em>et al</em>. <a href="http://genome.cshlp.org/content/15/8/1034" target="_blank"> Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes</a>. <em>Genome Res</em>. 2005 Aug;15(8):1034-50. </p> <h3>Chain/Net:</h3> <p> Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. <a href="http://www.pnas.org/content/100/20/11484.abstract" target="_blank"> Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes</a>. <em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9. </p> <h3>Multiz:</h3> <p> Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, <em>et al</em>. <a href="http://genome.cshlp.org/content/14/4/708.abstract" target="_blank"> Aligning multiple genomic sequences with the threaded blockset aligner</a>. <em>Genome Res</em>. 2004 Apr;14(4):708-15. </p> <p> Harris RS. <a href="http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf" target="_blank">Improved pairwise alignment of genomic DNA</a>. <em>Ph.D. Thesis</em>. Pennsylvania State University, USA. 2007. </p> <h3>Blastz:</h3> <p> Chiaromonte F, Yap VB, Miller W. <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank"> Scoring pairwise genomic sequence alignments</a>. <em>Pac Symp Biocomput</em>. 2002;:115-26. </p> <p> Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. <a href="http://genome.cshlp.org/content/13/1/103.abstract" target="_blank"> Human-mouse alignments with BLASTZ</a>. <em>Genome Res</em>. 2003 Jan;13(1):103-7. </p>