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/eboVir2/cons49way.html src/hg/makeDb/trackDb/ebola/eboVir2/cons49way.html index b2620e999d7..be3e414958e 100644 --- src/hg/makeDb/trackDb/ebola/eboVir2/cons49way.html +++ src/hg/makeDb/trackDb/ebola/eboVir2/cons49way.html @@ -1,166 +1,178 @@ <H2>Description</H2> <P> 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/<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 the tree topology from Gire et.al (2014): <pre> (((((((((((((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)) </pre> <pre> (((((((((((((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)) </pre> Framing tables 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=eboVir2&hgta_group=compGeno&hgta_track=cons49way">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=eboVir2">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>