This track shows multiple alignments of 369 bacteria, 362 Staphylococcus aureus, one Bacillus subtilis and six Escherichia coli, and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package, for all 369 species. The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are also displayed in this track.
The phylogenetic tree was derived from kmers in common counting between the sequences to obtain a 'distance' matrix, then using the phylip command 'neighbors' operation for the simple neighbor joining algorithm to establish this binary tree. This tree is not necessarily biologically correct, but it does serve as a useful guide tree for the multiz alignment procedure. See also: Phylip distance operations, assembly and alignment-free phylogeny reconstruction, and recapitulating phylogenies using k-mers.
Download data available at: hgdownload-test.
PhastCons (which has been used in previous Conservation tracks) is a hidden Markov model-based method that estimates the probability that each nucleotide belongs to a conserved element, based on the multiple alignment. It considers not just each individual alignment column, but also its flanking columns. By contrast, phyloP separately measures conservation at individual columns, ignoring the effects of their neighbors. As a consequence, the phyloP plots have a less smooth appearance than the phastCons plots, with more "texture" at individual sites. The two methods have different strengths and weaknesses. PhastCons is sensitive to "runs" of conserved sites, and is therefore effective for picking out conserved elements. PhyloP, on the other hand, is more appropriate for evaluating signatures of selection at particular nucleotides or classes of nucleotides (e.g., third codon positions, or first positions of miRNA target sites).
Another important difference is that phyloP can measure acceleration (faster evolution than expected under neutral drift) as well as conservation (slower than expected evolution). In the phyloP plots, sites predicted to be conserved are assigned positive scores (and shown in blue), while sites predicted to be fast-evolving are assigned negative scores (and shown in red). The absolute values of the scores represent -log p-values under a null hypothesis of neutral evolution. The phastCons scores, by contrast, represent probabilities of negative selection and range between 0 and 1.
Both phastCons and phyloP treat alignment gaps and unaligned nucleotides as missing data.
See also: lastz parameters and other details, and chain minimum score and gap parameters used in these alignments.
Missing sequence in the assemblies is highlighted in the track display by regions of yellow when zoomed out and Ns displayed at base level (see Gap Annotation, below).
Downloads for data in this track are available:
Organism
NCBI assemblySpecies Assembly name browser or
NCBI sourceStaph/GCF_000013465.1
reference sequenceStaphylococcus aureus Feb. 2006 (USA300_FPR3757/staAur2) Feb. 2006 (USA300_FPR3757/staAur2) ***** % 99 reference identity ***** Sa_USA300_SUR15 Staphylococcus aureus Feb. 2017 (ASM200068v1) GCF_002000685.1 Sa_USA300_SUR24 Staphylococcus aureus Feb. 2017 (ASM200086v1) GCF_002000865.1 ***** % 98 reference identity ***** Sa_USA300_SUR9 Staphylococcus aureus Feb. 2017 (ASM200056v1) GCF_002000565.1 Sa_USA300_SUR10 Staphylococcus aureus Feb. 2017 (ASM200058v1) GCF_002000585.1 Sa_USA300_SUR11 Staphylococcus aureus Feb. 2017 (ASM200060v1) GCF_002000605.1 Sa_USA300_SUR4 Staphylococcus aureus Feb. 2017 (ASM359542v1) GCF_003595425.1 Sa_USA300_SUR8 Staphylococcus aureus Feb. 2017 (ASM359550v1) GCF_003595505.1 Sa_USA300_NRS384 Staphylococcus aureus subsp. aureus USA300 Mar. 2018 (ASM299386v1) GCF_002993865.1 Sa_1971C01 Staphylococcus aureus subsp. aureus Feb. 2018 (ASM171768v3) GCF_001717685.1 Sa_USA300_SUR13 Staphylococcus aureus Feb. 2017 (ASM200064v1) GCF_002000645.1 Sa_USA300_SUR21 Staphylococcus aureus Feb. 2017 (ASM200080v1) GCF_002000805.1 Sa_USA300_SUR3 Staphylococcus aureus Feb. 2017 (ASM359540v1) GCF_003595405.1 Sa_USA300_SUR6 Staphylococcus aureus Feb. 2017 (ASM359546v1) GCF_003595465.1 Sa_USA300_SUR7 Staphylococcus aureus Feb. 2017 (ASM359548v1) GCF_003595485.1 Sa_USA300_TCH1516 Staphylococcus aureus subsp. aureus USA300_TCH1516 Mar. 2009 (ASM1708v1) GCF_000017085.1 Sa_AR_0216 Staphylococcus aureus Jun. 2018 (ASM319372v1) GCF_003193725.1 Sa_USA300_SUR14 Staphylococcus aureus Feb. 2017 (ASM200066v1) GCF_002000665.1 Sa_USA300_SUR16 Staphylococcus aureus Feb. 2017 (ASM200070v1) GCF_002000705.1 Sa_USA300_SUR17 Staphylococcus aureus Feb. 2017 (ASM200072v1) GCF_002000725.1 Sa_USA300_SUR18 Staphylococcus aureus Feb. 2017 (ASM200074v1) GCF_002000745.1 Sa_USA300_SUR19 Staphylococcus aureus Feb. 2017 (ASM200076v1) GCF_002000765.1 Sa_USA300_SUR20 Staphylococcus aureus Feb. 2017 (ASM200078v1) GCF_002000785.1 Sa_USA300_SUR22 Staphylococcus aureus Feb. 2017 (ASM200082v1) GCF_002000825.1 Sa_USA300_SUR23 Staphylococcus aureus Feb. 2017 (ASM200084v1) GCF_002000845.1 Sa_USA300_ISMMS1 Staphylococcus aureus USA300-ISMMS1 Feb. 2014 (ASM56845v1) GCF_000568455.1 Sa_UTSW_MRSA_55 Staphylococcus aureus Mar. 2016 (ASM158051v1) GCF_001580515.1 Sa_USA300_SUR12 Staphylococcus aureus Feb. 2017 (ASM200062v1) GCF_002000625.1 Sa_1625CO1 Staphylococcus aureus subsp. aureus Dec. 2017 (ASM171772v2) GCF_001717725.1 Sa_AR_0226 Staphylococcus aureus Jun. 2018 (ASM320359v1) GCF_003203595.1 Sa_29b_MRSA Staphylococcus aureus Jan. 2015 (ASM81504v1) GCF_000815045.1 Sa_31b_MRSA Staphylococcus aureus Jan. 2015 (ASM81508v1) GCF_000815085.1 Sa_33b Staphylococcus aureus Jan. 2015 (ASM81512v1) GCF_000815125.1 Sa_26b_MRSA Staphylococcus aureus Jan. 2015 (ASM81516v1) GCF_000815165.1 Sa_25b_MRSA Staphylococcus aureus Jan. 2015 (ASM81520v1) GCF_000815205.1 Sa_27b_MRSA Staphylococcus aureus Jan. 2015 (ASM81524v1) GCF_000815245.1 Sa_UA_S391_USA300 Staphylococcus aureus May 2014 (ASM69587v1) GCF_000695875.1 Sa_C2406 Staphylococcus aureus Apr. 2017 (ASM208899v1) GCF_002088995.1 Sa_CIT Staphylococcus aureus subsp. aureus Apr. 2018 (ASM307339v1) GCF_003073395.1 Sa_OXLIM Staphylococcus aureus subsp. aureus Apr. 2018 (ASM307343v1) GCF_003073435.1 Sa_JE2 Staphylococcus aureus Apr. 2017 (ASM208552v1) GCF_002085525.1 Sa_1969N Staphylococcus aureus subsp. aureus Jan. 2018 (ASM171770v2) GCF_001717705.1 Sa_3020C01 Staphylococcus aureus subsp. aureus Jan. 2018 (ASM173565v2) GCF_001735655.2 Sa_USA300_2014C02 Staphylococcus aureus subsp. aureus Jan. 2018 (ASM118372v2) GCF_001183725.2 Sa_USA300_SUR1_a Staphylococcus aureus subsp. aureus Jan. 2017 (ASM195681v1) GCF_001956815.1 Sa_USA300_SUR1_b Staphylococcus aureus Feb. 2017 (ASM359536v1) GCF_003595365.1 Sa_USA300_SUR2 Staphylococcus aureus Feb. 2017 (ASM359538v1) GCF_003595385.1 Sa_FDAARGOS_140 Staphylococcus aureus Mar. 2018 (ASM147171v2) GCF_001471715.2 Sa_2148C01 Staphylococcus aureus subsp. aureus Jan. 2018 (ASM171797v3) GCF_001717975.2 Sa_USA300_2014C01 Staphylococcus aureus subsp. aureus Feb. 2018 (ASM118370v3) GCF_001183705.3 ***** % 97 reference identity ***** Sa_5118N Staphylococcus aureus subsp. aureus Feb. 2018 (ASM171764v3) GCF_001717645.1 Sa_CA15 Staphylococcus aureus Jun. 2015 (ASM102189v1) GCF_001021895.1 Sa_AR_0223 Staphylococcus aureus Jun. 2018 (ASM319368v1) GCF_003193685.1 Sa_CAR Staphylococcus aureus subsp. aureus Apr. 2018 (ASM307341v1) GCF_003073415.1 Sa_HUV05 Staphylococcus aureus Oct. 2015 (ASM104599v2) GCF_001045995.2 Sa_2395_USA500 Staphylococcus aureus Aug. 2014 (ASM74650v1) GCF_000746505.1 Sa_M1 Staphylococcus aureus M1 Apr. 2013 (ASM36774v1) GCF_000367745.1 Sa_OC8 Staphylococcus aureus Oct. 2016 (ASM235535v1) GCF_002355355.1 Sa_199 Staphylococcus aureus Aug. 2018 (ASM342554v1) GCF_003425545.1 Sa_64 Staphylococcus aureus Aug. 2018 (ASM342591v1) GCF_003425915.1 ***** % 96 reference identity ***** Sa_AR_0225 Staphylococcus aureus Jun. 2018 (ASM319396v1) GCF_003193965.1 Sa_EDCC5458 Staphylococcus aureus subsp. aureus Nov. 2017 (ASM278646v1) GCF_002786465.1 Sa_NCTC13394 Staphylococcus aureus Jun. 2018 (40677_F01) GCF_900474525.1 Sa_28 Staphylococcus aureus Aug. 2018 (ASM342583v1) GCF_003425835.1 Sa_82 Staphylococcus aureus Aug. 2018 (ASM342588v1) GCF_003425885.1 Sa_SVH7513 Staphylococcus aureus May 2018 (ASM311172v1) GCF_003111725.1 Sa_NRS120 Staphylococcus aureus Jan. 2018 (ASM101948v2) GCF_001019485.2 Sa_V2200 Staphylococcus aureus Oct. 2015 (ASM104609v2) GCF_001046095.2 Sa_MI Staphylococcus aureus Jan. 2016 (ASM154841v1) GCF_001548415.1 Sa_TCH_959 Staphylococcus aureus Jan. 2018 (ASM101868v2) GCF_001018685.2 Sa_COL Staphylococcus aureus subsp. aureus COL May 2005 (ASM1204v1) GCF_000012045.1 Sa_FDAARGOS_5 Staphylococcus aureus subsp. aureus Feb. 2018 (ASM62661v3) GCF_000626615.2 Sa_NCTC13140 Staphylococcus aureus Jun. 2018 (40677_A01) GCF_900474725.1 Sa_Gv88 Staphylococcus aureus subsp. aureus Jan. 2016 (ASM151570v1) GCF_001515705.1 Sa_Gv51 Staphylococcus aureus subsp. aureus Jan. 2016 (ASM151566v1) GCF_001515665.1 ***** % 95 reference identity ***** Sa_164 Staphylococcus aureus Aug. 2018 (ASM335488v1) GCF_003354885.1 Sa_HC1335 Staphylococcus aureus subsp. aureus Jan. 2016 (ASM151576v1) GCF_001515765.1 Sa_Gv69 Staphylococcus aureus subsp. aureus Oct. 2014 (ASM76957v1) GCF_000769575.1 Sa_JMUB3031 Staphylococcus aureus Aug. 2018 (ASM357383v1) GCF_003573835.1 Sa_Be62 Staphylococcus aureus subsp. aureus Jan. 2016 (ASM151568v1) GCF_001515685.1 Sa_HC1340 Staphylococcus aureus subsp. aureus Jan. 2016 (ASM151574v1) GCF_001515745.1 Sa_Bmb9393 Staphylococcus aureus Jul. 2013 (ASM41834v1) GCF_000418345.1 Sa_USA400_0051 Staphylococcus aureus Nov. 2017 (ASM279528v1) GCF_002795285.1 Sa_UCI62 Staphylococcus aureus subsp. aureus Jan. 2017 (ASM197500v1) GCF_001975005.1 Sa_AR_0468 Staphylococcus aureus Jun. 2018 (ASM320361v1) GCF_003203615.1 Sa_AR_0467 Staphylococcus aureus Jun. 2018 (ASM319388v1) GCF_003193885.1 Sa_JH1 Staphylococcus aureus subsp. aureus JH1 Jun. 2007 (ASM1712v1) GCF_000017125.1 Sa_AR_474 Staphylococcus aureus Jul. 2018 (ASM333090v1) GCF_003330905.1 Sa_AR465 Staphylococcus aureus Apr. 2018 (ASM307365v1) GCF_003073655.1 Sa_JH9 Staphylococcus aureus subsp. aureus JH9 May 2007 (ASM1680v1) GCF_000016805.1 Sa_HPV107 Staphylococcus aureus Jan. 2018 (ASM101957v2) GCF_001019575.2 Sa_AR_0215 Staphylococcus aureus Jun. 2018 (ASM319402v1) GCF_003194025.1 Sa_ZJ5499 Staphylococcus aureus May 2016 (ASM164088v1) GCF_001640885.1 Sa_Sa_Newman_UoM Staphylococcus aureus Jul. 2016 (Sa_Newman_UoM) GCF_900092595.1 Sa_Newman Staphylococcus aureus subsp. aureus str. Newman Jul. 2007 (ASM1046v1) GCF_000010465.1 Sa_Newman_D2C Staphylococcus aureus subsp. aureus Sep. 2017 (ASM231039v1) GCF_002310395.1 Sa_Newman_NYU_Newman Staphylococcus aureus subsp. aureus str. Newman Sep. 2017 (ASM231043v1) GCF_002310435.1 Sa_AR461 Staphylococcus aureus Apr. 2018 (ASM307371v1) GCF_003073715.1 Sa_NRS271 Staphylococcus aureus Jan. 2018 (ASM101883v2) GCF_001018835.2 Sa_SA112 Staphylococcus aureus Apr. 2018 (ASM302966v1) GCF_003029665.1 Sa_FDAARGOS_412 Staphylococcus aureus Sep. 2017 (ASM238624v1) GCF_002386245.1 Sa_NCTC9944 Staphylococcus aureus Jun. 2018 (40415_F02) GCF_900474575.1 Sa_545 Staphylococcus aureus Aug. 2018 (ASM335494v1) GCF_003354945.1 Sa_MSSA54 Staphylococcus aureus Nov. 2018 (ASM379818v1) GCF_003798185.1 Sa_FDAARGOS_43 Staphylococcus aureus Feb. 2018 (ASM101912v2) GCF_001019125.2 Sa_Mw2_2018 Staphylococcus aureus Jan. 2018 (ASM101953v2) GCF_001019535.2 Sa_FCFHV36 Staphylococcus aureus Apr. 2015 (ASM96922v1) GCF_000969225.1 Sa_MW2_2004 Staphylococcus aureus subsp. aureus MW2 May 2004 (ASM1126v1) GCF_000011265.1 Sa_546 Staphylococcus aureus Aug. 2018 (ASM335496v1) GCF_003354965.1 Sa_FDAARGOS_1 Staphylococcus aureus Feb. 2018 (ASM101925v2) GCF_001019255.2 Sa_54 Staphylococcus aureus Aug. 2018 (ASM335480v1) GCF_003354805.1 Sa_T0131 Staphylococcus aureus subsp. aureus T0131 Apr. 2011 (ASM20466v1) GCF_000204665.1 Sa_165 Staphylococcus aureus Aug. 2018 (ASM335466v1) GCF_003354665.1 Sa_FDAARGOS_48 Staphylococcus aureus Feb. 2018 (ASM101920v2) GCF_001019205.2 Sa_NCTC13277 Staphylococcus aureus Jun. 2018 (35910_A02) GCF_900478245.1 Sa_MRSA252 Staphylococcus aureus subsp. aureus MRSA252 Jun. 2004 (ASM1150v1) GCF_000011505.1 Sa_WCH_SK2 Staphylococcus aureus Aug. 2018 (ASM339410v1) GCF_003394105.1 ***** % 94 reference identity ***** Sa_H_EMRSA_15 Staphylococcus aureus subsp. aureus May 2014 (ASM69521v1) GCF_000695215.1 Sa_MRSA107 Staphylococcus aureus Jan. 2018 (ASM289538v1) GCF_002895385.1 Sa_V521 Staphylococcus aureus May 2016 (ASM164102v1) GCF_001641025.1 Sa_GR2 Staphylococcus aureus subsp. aureus Sep. 2015 (ASM129698v1) GCF_001296985.1 Sa_NMR08 Staphylococcus aureus Oct. 2017 (ASM240710v1) GCF_002407105.1 Sa_NCTC13395 Staphylococcus aureus Jun. 2018 (40871_F01) GCF_900474735.1 Sa_NZAK3 Staphylococcus aureus Jan. 2016 (NZAK3) GCF_900017775.1 Sa_AR_0472 Staphylococcus aureus Jun. 2018 (ASM319366v1) GCF_003193665.1 Sa_11819_97 Staphylococcus aureus subsp. aureus 11819-97 Dec. 2011 (ASM23923v1) GCF_000239235.1 Sa_NCTC13435 Staphylococcus aureus Mar. 2015 (NCTC13435) GCF_001457495.1 Sa_JKD6008 Staphylococcus aureus subsp. aureus str. JKD6008 Aug. 2010 (ASM14559v1) GCF_000145595.1 Sa_AR_0473 Staphylococcus aureus Jun. 2018 (ASM319378v1) GCF_003193785.1 Sa_NCCP14562 Staphylococcus aureus May 2016 (ASM164092v1) GCF_001640925.1 Sa_NCCP14558 Staphylococcus aureus May 2016 (ASM164090v1) GCF_001640905.1 Sa_HO_5096_0412 Staphylococcus aureus subsp. aureus HO 5096 0412 Apr. 2012 (ASM28453v1) GCF_000284535.1 Sa_JKD6159 Staphylococcus aureus subsp. aureus JKD6159 Aug. 2010 (ASM14495v1) GCF_000144955.1 Sa_AR_0219 Staphylococcus aureus Jun. 2018 (ASM319370v1) GCF_003193705.1 Sa_Mu50 Staphylococcus aureus subsp. aureus Mu50 May 2004 (ASM966v1) GCF_000009665.1 Sa_MOZ66 Staphylococcus aureus Aug. 2018 (ASM342614v1) GCF_003426145.1 Sa_ED98 Staphylococcus aureus subsp. aureus ED98 Oct. 2009 (ASM2458v1) GCF_000024585.1 Sa_Z172 Staphylococcus aureus subsp. aureus Z172 Oct. 2013 (ASM48588v1) GCF_000485885.1 Sa_M121 Staphylococcus aureus Jun. 2015 (ASM102187v1) GCF_001021875.1 Sa_TW20 Staphylococcus aureus subsp. aureus TW20 Nov. 2009 (ASM2704v1) GCF_000027045.1 Sa_CA12 Staphylococcus aureus Oct. 2015 (ASM104579v2) GCF_001045795.2 Sa_FORC_027 Staphylococcus aureus Sep. 2016 (ASM172596v1) GCF_001725965.1 Sa_MSSA476 Staphylococcus aureus subsp. aureus MSSA476 Jun. 2004 (ASM1152v1) GCF_000011525.1 Sa_FDAARGOS_2 Staphylococcus aureus Feb. 2018 (ASM101864v2) GCF_001018645.2 Sa_FORC_062 Staphylococcus aureus Aug. 2018 (ASM335192v1) GCF_003351925.1 Sa_AR_0228 Staphylococcus aureus Jun. 2018 (ASM320363v1) GCF_003203635.1 Sa_187 Staphylococcus aureus Aug. 2018 (ASM335456v1) GCF_003354565.1 Sa_629 Staphylococcus aureus Aug. 2018 (ASM335458v1) GCF_003354585.1 Sa_FDAARGOS_40 Staphylococcus aureus Feb. 2018 (ASM101949v2) GCF_001019495.2 Sa_61 Staphylococcus aureus Aug. 2018 (ASM335470v1) GCF_003354705.1 Sa_191 Staphylococcus aureus Aug. 2018 (ASM335476v1) GCF_003354765.1 Sa_628 Staphylococcus aureus Aug. 2018 (ASM335498v1) GCF_003354985.1 Sa_UCI_28_ST5 Staphylococcus aureus subsp. aureus Jan. 2017 (ASM197504v1) GCF_001975045.1 Sa_CMRSA_3 Staphylococcus aureus Jun. 2018 (ASM326477v1) GCF_003264775.1 Sa_Clinical Staphylococcus aureus subsp. aureus Dec. 2016 (PP_HGAG_QV30_2SC_T4) GCF_900129335.1 Sa_17_LA_343 Staphylococcus aureus Jul. 2018 (17_LA_343) GCF_900324345.1 Sa_Mu3 Staphylococcus aureus subsp. aureus Mu3 Sep. 2007 (ASM1044v1) GCF_000010445.1 Sa_AR_0220 Staphylococcus aureus Jun. 2018 (ASM320367v1) GCF_003203675.1 Sa_NRS1 Staphylococcus aureus Jan. 2018 (ASM101943v2) GCF_001019435.2 Sa_ISU935_ST5 Staphylococcus aureus Jun. 2017 (ASM220455v1) GCF_002204555.1 Sa_CR14_035 Staphylococcus aureus Apr. 2018 (ASM303146v1) GCF_003031465.1 Sa_ST228_16125 Staphylococcus aureus subsp. aureus ST228 Oct. 2012 (ASM38298v1) GCF_000382985.1 Sa_MN8 Staphylococcus aureus subsp. aureus MN8 Jun. 2010 (ASM16019v1) GCF_000160195.1 Sa_04_02981 Staphylococcus aureus 04-02981 Nov. 2010 (ASM2514v1) GCF_000025145.1 Sa_N315 Staphylococcus aureus subsp. aureus N315 May 2004 (ASM964v1) GCF_000009645.1 Sa_NRS484 Staphylococcus aureus Jan. 2018 (ASM101939v2) GCF_001019395.2 Sa_CA_347 Staphylococcus aureus CA-347 Jun. 2013 (ASM41277v1) GCF_000412775.1 Sa_7_4623 Staphylococcus aureus Jul. 2018 (7_4623) GCF_900324225.1 Sa_HOU1444_VR Staphylococcus aureus Sep. 2015 (ASM127874v1) GCF_001278745.1 Sa_FORC_045 Staphylococcus aureus Jun. 2017 (ASM220932v1) GCF_002209325.1 Sa_DSM_20231 Staphylococcus aureus subsp. aureus DSM 20231 Jun. 2015 (ASM102710v1) GCF_001027105.1 Sa_9_LA_281 Staphylococcus aureus Jul. 2018 (9_LA_281) GCF_900324265.1 Sa_NCTC11940 Staphylococcus aureus Jun. 2018 (42197_E02) GCF_900475055.1 Sa_NRS70 Staphylococcus aureus Jan. 2018 (ASM101930v2) GCF_001019305.2 Sa_AR462 Staphylococcus aureus Apr. 2018 (ASM307377v1) GCF_003073775.1 Sa_0201753_2 Staphylococcus aureus Jun. 2018 (ASM319418v1) GCF_003194185.1 Sa_CFSAN007850 Staphylococcus aureus Oct. 2017 (ASM263380v1) GCF_002633805.1 Sa_NCTC6136 Staphylococcus aureus Jun. 2018 (41004_D01) GCF_900474715.1 Sa_1_1439 Staphylococcus aureus Jul. 2018 (1_1439) GCF_900324205.1 Sa_RIVM6519 Staphylococcus aureus Apr. 2016 (ASM161830v1) GCF_001618305.1 Sa_CHU15_056 Staphylococcus aureus Jun. 2018 (ASM319440v1) GCF_003194405.1 ***** % 93 reference identity ***** Sa_ch22 Staphylococcus aureus Jul. 2018 (ASM335060v1) GCF_003350605.1 Sa_22_LA_562 Staphylococcus aureus Jul. 2018 (22_LA_562) GCF_900324415.1 Sa_ch21 Staphylococcus aureus Jul. 2018 (ASM334315v1) GCF_003343155.1 Sa_M92 Staphylococcus aureus Jun. 2018 (ASM209759v2) GCF_002097595.2 Sa_5_3949 Staphylococcus aureus Jul. 2018 (5_3949) GCF_900324235.1 Sa_FORC_039 Staphylococcus aureus May 2017 (ASM214011v1) GCF_002140115.1 Sa_CFSAN007896 Staphylococcus aureus Apr. 2018 (ASM303142v1) GCF_003031425.1 Sa_FORC_012 Staphylococcus aureus Mar. 2016 (ASM158049v1) GCF_001580495.1 Sa_JH4899 Staphylococcus aureus Mar. 2017 (ASM235667v1) GCF_002356675.1 Sa_CN1 Staphylococcus aureus subsp. aureus CN1 Aug. 2013 (ASM46305v1) GCF_000463055.1 Sa_SR434 Staphylococcus aureus Feb. 2017 (ASM198613v1) GCF_001986135.1 Sa_CC5 Staphylococcus aureus Apr. 2018 (ASM303148v1) GCF_003031485.1 Sa_FDAARGOS_159 Staphylococcus aureus Feb. 2018 (ASM155879v2) GCF_001558795.2 Sa_12_LA_293 Staphylococcus aureus Jul. 2018 (12_LA_293) GCF_900324315.1 Sa_FORC_040 Staphylococcus aureus Jul. 2017 (ASM221466v1) GCF_002214665.1 Sa_NRS153 Staphylococcus aureus Jan. 2018 (ASM101884v2) GCF_001018845.2 Sa_FORC_001 Staphylococcus aureus subsp. aureus Nov. 2014 (ASM77202v1) GCF_000772025.1 Sa_15_LA_305 Staphylococcus aureus Jul. 2018 (15_LA_305) GCF_900324335.1 Sa_FDAARGOS_504 Staphylococcus aureus Nov. 2018 (ASM382791v1) GCF_003827915.1 Sa_TMUS2126 Staphylococcus aureus subsp. aureus Mar. 2015 (ASM154965v1) GCF_001549655.1 Sa_TMUS2134 Staphylococcus aureus subsp. aureus Mar. 2015 (ASM154967v1) GCF_001549675.1 Sa_CFSAN064038 Staphylococcus aureus Apr. 2018 (ASM302964v1) GCF_003029645.1 Sa_13_LA_301 Staphylococcus aureus Jul. 2018 (13_LA_301) GCF_900324305.1 Sa_14_5418 Staphylococcus aureus Jul. 2018 (14_5418) GCF_900324325.1 Sa_SA564 Staphylococcus aureus Sep. 2015 (ASM128114v1) GCF_001281145.1 Sa_21_LA_436 Staphylococcus aureus Jul. 2018 (21_LA_436) GCF_900324405.1 Sa_8_LA_272 Staphylococcus aureus Jul. 2018 (8_LA_272) GCF_900324245.1 Sa_20_LA_415 Staphylococcus aureus Jul. 2018 (20_LA_415) GCF_900324385.1 Sa_AR_0470 Staphylococcus aureus Jun. 2018 (ASM319374v1) GCF_003193745.1 Sa_ED133 Staphylococcus aureus subsp. aureus ED133 Jun. 2010 (ASM21031v1) GCF_000210315.1 Sa_TCH60 Staphylococcus aureus subsp. aureus TCH60 Nov. 2010 (ASM15953v2) GCF_000159535.2 Sa_2_LA_86 Staphylococcus aureus Jul. 2018 (2_LA_86) GCF_900324255.1 Sa_3_LA_115 Staphylococcus aureus Jul. 2018 (3_LA_115) GCF_900324215.1 Sa_ECT_R_2 Staphylococcus aureus subsp. aureus ECT-R 2 Nov. 2010 (ASM25313v1) GCF_000253135.1 Sa_19_LA_388 Staphylococcus aureus Jul. 2018 (19_LA_388) GCF_900324365.1 Sa_6_LA_232 Staphylococcus aureus Jul. 2018 (6_LA_232) GCF_900324275.1 Sa_MOK063 Staphylococcus aureus Jun. 2018 (ASM318610v1) GCF_003186105.1 Sa_CFSAN018749 Staphylococcus aureus Apr. 2018 (ASM303006v1) GCF_003030065.1 Sa_2148N Staphylococcus aureus subsp. aureus Jan. 2018 (ASM171766v2) GCF_001717665.1 Sa_NCTC10344 Staphylococcus aureus Jun. 2018 (41236_E02) GCF_900474755.1 Sa_MOK042 Staphylococcus aureus Jun. 2018 (ASM318612v1) GCF_003186125.1 Sa_CFSAN007851 Staphylococcus aureus Oct. 2017 (ASM263382v1) GCF_002633825.1 Sa_E16SA093 Staphylococcus aureus Jul. 2018 (ASM334273v1) GCF_003342735.1 Sa_ST228_16035 Staphylococcus aureus subsp. aureus ST228 Oct. 2012 (ASM38296v1) GCF_000382965.1 Sa_ST228_10388 Staphylococcus aureus subsp. aureus ST228 Oct. 2012 (ASM96732v1) GCF_000967325.1 Sa_ST228_10497 Staphylococcus aureus subsp. aureus ST228 Oct. 2012 (ASM96734v1) GCF_000967345.1 Sa_ST228_15532 Staphylococcus aureus subsp. aureus ST228 Oct. 2012 (ASM96736v1) GCF_000967365.1 Sa_ST228_18341 Staphylococcus aureus subsp. aureus ST228 Oct. 2012 (ASM96738v1) GCF_000967385.1 Sa_55_99_44 Staphylococcus aureus Dec. 2017 (ASM280388v1) GCF_002803885.1 Sa_ST228_18583 Staphylococcus aureus subsp. aureus ST228 Oct. 2012 (ASM38300v1) GCF_000383005.1 Sa_ST228_18412 Staphylococcus aureus subsp. aureus ST228 Oct. 2012 (ASM96740v1) GCF_000967405.1 Sa_080880048_3 Staphylococcus aureus Jun. 2018 (ASM319406v1) GCF_003194065.1 Sa_101110051_1 Staphylococcus aureus Jun. 2018 (ASM319414v1) GCF_003194145.1 Sa_FDA209P Staphylococcus aureus Sep. 2015 (ASM154829v1) GCF_001548295.1 Sa_ATCC_6538 Staphylococcus aureus subsp. aureus Mar. 2017 (ASM202514v1) GCF_002025145.1 Sa_SA268 Staphylococcus aureus subsp. aureus SA268 Aug. 2014 (ASM73761v1) GCF_000737615.1 Sa_CMRSA_6 Staphylococcus aureus Jun. 2018 (ASM326481v1) GCF_003264815.1 Sa_XQ Staphylococcus aureus Nov. 2015 (ASM144434v1) GCF_001444345.1 Sa_CFSAN007847 Staphylococcus aureus Oct. 2017 (ASM263378v1) GCF_002633785.1 Sa_78 Staphylococcus aureus Aug. 2018 (ASM335490v1) GCF_003354905.1 Sa_BA01611 Staphylococcus aureus Mar. 2017 (ASM129832v2) GCF_001298325.2 Sa_ST772_MRSA_V_DAR4145 Staphylococcus aureus subsp. aureus ST772-MRSA-V Jan. 2015 (ASM82803v1) GCF_000828035.1 Sa_AR_0469 Staphylococcus aureus Jun. 2018 (ASM319400v1) GCF_003194005.1 Sa_FORC_061 Staphylococcus aureus Jul. 2018 (ASM334705v1) GCF_003347055.1 Sa_ST398_S0385 Staphylococcus aureus subsp. aureus ST398 Jan. 2010 (ASM958v1) GCF_000009585.1 Sa_QD_CD9 Staphylococcus aureus Aug. 2018 (ASM343236v1) GCF_003432365.1 Sa_S_aureus_171 Staphylococcus aureus Apr. 2018 (171) GCF_900240125.1 Sa_101110041_3 Staphylococcus aureus Jun. 2018 (ASM319416v1) GCF_003194165.1 Sa_O17 Staphylococcus aureus Sep. 2018 (ASM349012v1) GCF_003490125.1 Sa_AR_475 Staphylococcus aureus Jul. 2018 (ASM328839v1) GCF_003288395.1 Sa_NRS143 Staphylococcus aureus Jan. 2018 (ASM101897v2) GCF_001018975.2 Sa_SA40TW Staphylococcus aureus Nov. 2016 (ASM188026v1) GCF_001880265.1 Sa_GD705 Staphylococcus aureus Jul. 2018 (ASM208907v2) GCF_002089075.2 Sa_13420 Staphylococcus aureus Jun. 2018 (ASM319410v1) GCF_003194105.1 Sa_CFBR_105 Staphylococcus aureus Aug. 2018 (ASM343136v1) GCF_003431365.1 Sa_NCTC13137 Staphylococcus aureus Jun. 2018 (40657_E01) GCF_900474555.1 Sa_GN1 Staphylococcus aureus Oct. 2017 (ASM360991v1) GCF_003609915.1 Sa_AR464 Staphylococcus aureus Apr. 2018 (ASM307375v1) GCF_003073755.1 Sa_277 Staphylococcus aureus Aug. 2018 (ASM335468v1) GCF_003354685.1 Sa_85 Staphylococcus aureus Aug. 2018 (ASM335478v1) GCF_003354785.1 Sa_F17SA003 Staphylococcus aureus Jul. 2018 (ASM334277v1) GCF_003342775.1 Sa_27 Staphylococcus aureus Aug. 2018 (ASM335454v1) GCF_003354545.1 Sa_O46 Staphylococcus aureus O46 Dec. 2017 (ASM18945v3) GCF_000189455.2 Sa_No10 Staphylococcus aureus Jun. 2017 (ASM235665v1) GCF_002356655.1 Sa_08_02300 Staphylococcus aureus Jun. 2016 (ASM165607v1) GCF_001656075.1 ***** % 92 reference identity ***** Sa_502A_RN6607 Staphylococcus aureus Mar. 2014 (ASM59796v1) GCF_000597965.1 Sa_IT1_S Staphylococcus aureus Jun. 2018 (ASM318498v1) GCF_003184985.1 Sa_IT4_R Staphylococcus aureus Jun. 2018 (ASM318500v1) GCF_003185005.1 Sa_CFSAN007894 Staphylococcus aureus Oct. 2017 (ASM263386v1) GCF_002633865.1 Sa_RIVM3897 Staphylococcus aureus Dec. 2015 (ASM146575v1) GCF_001465755.1 Sa_AR_0471 Staphylococcus aureus Jun. 2018 (ASM319376v1) GCF_003193765.1 Sa_FDAARGOS_10 Staphylococcus aureus Feb. 2018 (ASM101872v2) GCF_001018725.2 Sa_08_02119 Staphylococcus aureus Jun. 2016 (ASM165604v1) GCF_001656045.1 Sa_NX_T55 Staphylococcus aureus Aug. 2018 (ASM343234v1) GCF_003432345.1 Sa_NCTC8325_2018 Staphylococcus aureus subsp. aureus NCTC 8325 Jun. 2018 (43024_E01) GCF_900475245.1 Sa_HG001_RN1 Staphylococcus aureus subsp. aureus Dec. 2016 (ASM190018v1) GCF_001900185.1 Sa_NCTC8325_2006 Staphylococcus aureus subsp. aureus NCTC 8325 Feb. 2006 (ASM1342v1) GCF_000013425.1 Sa_O326 Staphylococcus aureus Oct. 2018 (ASM362783v1) GCF_003627835.1 Sa_AR466 Staphylococcus aureus Apr. 2018 (ASM307363v1) GCF_003073635.1 Sa_ILRI_Eymole1_1 Staphylococcus aureus Oct. 2014 (Staphylococcus_aureus_Sa_ILRI_217) GCF_000953255.1 Sa_NRS149 Staphylococcus aureus Jan. 2018 (ASM101877v2) GCF_001018775.2 Sa_BB155 Staphylococcus aureus Feb. 2016 (BB155) GCF_900004855.1 Sa_Tager_104 Staphylococcus aureus subsp. aureus Tager 104 Mar. 2016 (ASM45238v2) GCF_000452385.2 Sa_GD1539 Staphylococcus aureus Jul. 2018 (ASM208911v2) GCF_002089115.2 Sa_16_LA_309 Staphylococcus aureus Jul. 2018 (16_LA_309) GCF_900324295.1 Sa_SJTUF_J27 Staphylococcus aureus Jan. 2017 (ASM195675v1) GCF_001956755.1 Sa_HZW450 Staphylococcus aureus Oct. 2017 (ASM244297v1) GCF_002442975.1 Sa_JMUB1273 Staphylococcus aureus Aug. 2018 (ASM357385v1) GCF_003573855.1 Sa_121560027_1 Staphylococcus aureus Jun. 2018 (ASM319420v1) GCF_003194205.1 Sa_LA_MRSA_ST398_E154 Staphylococcus aureus subsp. aureus Nov. 2016 (ASM188707v1) GCF_001887075.1 Sa_45 Staphylococcus aureus Aug. 2018 (ASM335486v1) GCF_003354865.1 Sa_135 Staphylococcus aureus Aug. 2018 (ASM335492v1) GCF_003354925.1 Sa_PTDrAP2 Staphylococcus aureus May 2018 (ASM311174v1) GCF_003111745.1 Sa_FDAARGOS_6 Staphylococcus aureus Feb. 2018 (ASM101865v2) GCF_001018655.2 Sa_EDCC5464 Staphylococcus aureus subsp. aureus Nov. 2017 (ASM278653v1) GCF_002786535.1 Sa_ISU926_ST398 Staphylococcus aureus subsp. aureus Jun. 2017 (ASM220457v1) GCF_002204575.1 Sa_SA957 Staphylococcus aureus subsp. aureus SA957 Sep. 2013 (ASM47084v1) GCF_000470845.1 Sa_468 Staphylococcus aureus Aug. 2018 (ASM335462v1) GCF_003354625.1 Sa_466 Staphylococcus aureus Aug. 2018 (ASM335474v1) GCF_003354745.1 Sa_143 Staphylococcus aureus Aug. 2018 (ASM335472v1) GCF_003354725.1 Sa_M013 Staphylococcus aureus subsp. aureus M013 Dec. 2011 (ASM23712v1) GCF_000237125.1 Sa_08S00974 Staphylococcus aureus Mar. 2017 (ASM202512v1) GCF_002025125.1 Sa_NCTC5663 Staphylococcus aureus Jun. 2018 (41004_B01) GCF_900474695.1 Sa_ST20130942 Staphylococcus aureus Apr. 2016 (ASM161136v1) GCF_001611365.1 Sa_ST20130943 Staphylococcus aureus Apr. 2016 (ASM161138v1) GCF_001611385.1 Sa_NRS107 Staphylococcus aureus Jan. 2018 (ASM101927v2) GCF_001019275.2 Sa_RKI4 Staphylococcus aureus Jun. 2015 (ASM102704v1) GCF_001027045.1 Sa_JS395 Staphylococcus aureus subsp. aureus Oct. 2015 (ASM130723v1) GCF_001307235.1 Sa_422 Staphylococcus aureus Aug. 2018 (ASM335460v1) GCF_003354605.1 Sa_128 Staphylococcus aureus Aug. 2018 (ASM335464v1) GCF_003354645.1 Sa_24117_WT Staphylococcus aureus Aug. 2018 (24117-WT) GCF_900323905.1 Sa_24117_REV Staphylococcus aureus Aug. 2018 (24117-REV) GCF_900324045.1 Sa_24117_SCV Staphylococcus aureus Aug. 2018 (24117-SCV) GCF_900324065.1 Sa_GN3 Staphylococcus aureus Oct. 2017 (ASM360989v1) GCF_003609895.1 Sa_AUS0325 Staphylococcus aureus Sep. 2016 (AUS0325) GCF_900096745.1 Sa_ATCC_25923 Staphylococcus aureus subsp. aureus Sep. 2014 (ASM75620v1) GCF_000756205.1 Sa_Seattle_1945_G477 Staphylococcus aureus Jun. 2017 (ASM220207v1) GCF_002202075.1 Sa_Seattle_1945_G478 Staphylococcus aureus Jun. 2017 (ASM220209v1) GCF_002202095.1 Sa_10_5235 Staphylococcus aureus Jul. 2018 (10_5235) GCF_900324355.1 Sa_RIVM1295 Staphylococcus aureus Dec. 2015 (ASM146563v1) GCF_001465635.1 Sa_4_LA_208 Staphylococcus aureus Jul. 2018 (4_LA_208) GCF_900324285.1 Sa_NCTC3761 Staphylococcus aureus Jun. 2018 (40961_F01) GCF_900474675.1 Sa_08BA02176 Staphylococcus aureus 08BA02176 Sep. 2012 (ASM29659v1) GCF_000296595.1 Sa_GD1677 Staphylococcus aureus Jul. 2018 (ASM208909v2) GCF_002089095.2 Sa_1549_WT Staphylococcus aureus Aug. 2018 (1549-WT) GCF_900323925.1 Sa_1549_SCV Staphylococcus aureus Aug. 2018 (1549-SCV) GCF_900323965.1 Sa_1549_REV Staphylococcus aureus Aug. 2018 (1549-REV) GCF_900323955.1 Sa_FDAARGOS_15 Staphylococcus aureus Feb. 2018 (ASM101880v2) GCF_001018805.1 Sa_CFSAN007883 Staphylococcus aureus Oct. 2017 (ASM263384v1) GCF_002633845.1 ***** % 91 reference identity ***** Sa_NCTC8726 Staphylococcus aureus Jun. 2018 (41315_B01) GCF_900474565.1 Sa_AR_0222 Staphylococcus aureus Jun. 2018 (ASM320365v1) GCF_003203655.1 Sa_FORC_026 Staphylococcus aureus Nov. 2016 (ASM187954v1) GCF_001879545.1 Sa_CFSAN064037 Staphylococcus aureus Apr. 2018 (ASM303008v1) GCF_003030085.1 Sa_RF122 Staphylococcus aureus RF122 Nov. 2005 (ASM900v1) GCF_000009005.1 Sa_GD5 Staphylococcus aureus Apr. 2017 (ASM208905v1) GCF_002089055.1 Sa_FORC59 Staphylococcus aureus Mar. 2018 (ASM301087v1) GCF_003010875.1 Sa_SA40 Staphylococcus aureus subsp. aureus SA40 Sep. 2013 (ASM47086v1) GCF_000470865.1 Sa_LGA251 Staphylococcus aureus subsp. aureus LGA251 Aug. 2011 (ASM23726v1) GCF_000237265.1 Sa_293G Staphylococcus aureus Jul. 2018 (ASM208903v2) GCF_002089035.2 Sa_NRS137 Staphylococcus aureus Jan. 2018 (ASM101873v2) GCF_001018735.2 Sa_NCTC9752 Staphylococcus aureus Jun. 2018 (41236_D02) GCF_900474665.1 Sa_71193 Staphylococcus aureus subsp. aureus 71193 Apr. 2012 (ASM25868v1) GCF_000258685.1 Sa_K18 Staphylococcus aureus Jan. 2018 (ASM285041v1) GCF_002850415.1 Sa_K5 Staphylococcus aureus Feb. 2018 (ASM295201v1) GCF_002952015.1 Sa_RIVM1607 Staphylococcus aureus Dec. 2015 (ASM146567v1) GCF_001465675.1 Sa_VC40 Staphylococcus aureus subsp. aureus VC40 Feb. 2012 (ASM24549v1) GCF_000245495.1 Sa_NRS133 Staphylococcus aureus Jan. 2018 (ASM101891v2) GCF_001018915.2 Sa_NRS146 Staphylococcus aureus Jan. 2018 (ASM101941v2) GCF_001019415.2 Sa_ST20130938 Staphylococcus aureus Apr. 2016 (ASM161140v1) GCF_001611405.1 Sa_ST20130939 Staphylococcus aureus Apr. 2016 (ASM161142v1) GCF_001611425.1 Sa_NCTC7485 Staphylococcus aureus Jun. 2018 (40853_C01) GCF_900474535.1 Sa_CFSAN018750 Staphylococcus aureus Apr. 2018 (ASM303022v1) GCF_003030225.1 Sa_55_2053 Staphylococcus aureus subsp. aureus 55/2053 Aug. 2013 (ASM16033v2) GCF_000160335.2 Sa_80wphwpl_v1 Staphylococcus aureus Dec. 2018 (ASM385557v1) GCF_003855575.1 Sa_6850 Staphylococcus aureus subsp. aureus 6850 Aug. 2013 (ASM46295v1) GCF_000462955.1 ***** % 90 reference identity ***** Sa_MCRF184 Staphylococcus aureus Mar. 2016 (ASM159420v1) GCF_001594205.1 Sa_K17 Staphylococcus aureus Jan. 2018 (ASM285039v1) GCF_002850395.1 Sa_ST20130940 Staphylococcus aureus Apr. 2016 (ASM161132v1) GCF_001611325.1 Sa_ST20130941 Staphylococcus aureus Apr. 2016 (ASM161134v1) GCF_001611345.1 Sa_CFSAN007835 Staphylococcus aureus Oct. 2017 (ASM263376v1) GCF_002633765.1 ***** % 88 reference identity ***** Sa_MS4 Staphylococcus aureus Dec. 2015 (ASM145621v1) GCF_001456215.1 ***** others ***** Bacillus_subtilis_168 Bacillus subtilis subsp. subtilis str. 168 Mar. 2009 (ASM904v1) GCF_000009045.1 E_coli_K_12_MG1655 Escherichia coli str. K-12 substr. MG1655 Sep. 2013 (ASM584v2) GCF_000005845.2 E_coli_O157_H7_Sakai_RIMD_0509952 Escherichia coli O157:H7 str. Sakai Jun. 2018 (ASM886v2) GCF_000008865.2 E_coli_UMN026 Escherichia coli UMN026 Dec. 2008 (ASM2632v1) GCF_000026325.1 E_coli_O83_H1_NRG_857C Escherichia coli O83:H1 str. NRG 857C Nov. 2010 (ASM18334v1) GCF_000183345.1 E_coli_IAI39 Escherichia coli IAI39 Dec. 2008 (ASM2634v1) GCF_000026345.1 E_coli_O104_H4_2011C_3493 Escherichia coli O104:H4 str. 2011C-3493 Sep. 2012 (ASM29945v1) GCF_000299455.1
Table 1. Genome assemblies included in the 369-way Conservation track.
The track configuration options allow the user to display the three different sets of scores by all, subclass, individually, or any combination of these. In full and pack display modes, conservation scores are displayed as a wiggle track (histogram) in which the height reflects the value of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options.
Pairwise alignments of each species to the $organism genome are displayed below the conservation histogram as a grayscale density plot (in pack mode) or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons.
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). Note that excluding species from the pairwise display does not alter the the conservation score display.
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.
The Display chains between alignments configuration option enables display of gaps between alignment blocks in the pairwise alignments in a manner similar to the Chain track display. The following conventions are used:
Discontinuities in the genomic context (chromosome, scaffold or region) of the aligned DNA in the aligning species are shown as follows:
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:
Codon translation uses the following gene tracks as the basis for translation, depending on the species chosen (Table 2).
Table 2. Gene tracks used for codon translation.
Gene Track Species NCBI RefSeq genes all 369 genome sequences
Pairwise alignments with the $organism genome were generated for each species using lastz from repeat-masked genomic sequence. 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. Please note the specific parameters for the alignments. High-scoring chains were then placed along the genome, with gaps filled by lower-scoring chains, to produce an alignment net. For more information about the chaining and netting process and parameters for each species, see the description pages for the Chain and Net tracks.
The resulting best-in-genome pairwise alignments were progressively aligned using multiz/autoMZ, following the tree topology diagrammed above, to produce multiple alignments. The multiple alignments were post-processed to add annotations indicating alignment gaps, genomic breaks, and base quality of the component sequences. The annotated multiple alignments, in MAF format, are available for bulk download. An alignment summary table containing an entry for each alignment block in each species was generated to improve track display performance at large scales. Framing tables were constructed to enable visualization of codons in the multiple alignment display.
Both phastCons and phyloP are phylogenetic methods that rely on a tree model containing the tree topology, branch lengths representing evolutionary distance at neutrally evolving sites, the background distribution of nucleotides, and a substitution rate matrix. The all species tree model for this track was generated using the phyloFit program from the PHAST package (REV model, EM algorithm, medium precision) using multiple alignments of 4-fold degenerate sites extracted from the 369-way alignment (msa_view). The 4d sites were derived from the NCBI RefSeq gene set, filtered to select single-coverage long transcripts.
This same tree model was used in the phyloP calculations, however their background frequencies were modified to maintain reversibility. The resulting tree model for all species.
The phastCons program computes conservation scores based on a phylo-HMM, a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for conserved regions and a state for non-conserved regions. The value plotted at each site is the posterior probability that the corresponding alignment column was "generated" by the conserved state of the phylo-HMM. These scores reflect the phylogeny (including branch lengths) of the species in question, a continuous-time Markov model of the nucleotide substitution process, and a tendency for conservation levels to be autocorrelated along the genome (i.e., to be similar at adjacent sites). The general reversible (REV) substitution model was used. Unlike many conservation-scoring programs, phastCons does not rely on a sliding window of fixed size; therefore, short highly-conserved regions and long moderately conserved regions can both obtain high scores. More information about phastCons can be found in Siepel et al. 2005.
The phastCons parameters used were: expected-length=45, target-coverage=0.3, rho=0.3.
The phyloP program supports several different methods for computing p-values of conservation or acceleration, for individual nucleotides or larger elements ( http://compgen.cshl.edu/phast/). Here it was used to produce separate scores at each base (--wig-scores option), considering all branches of the phylogeny rather than a particular subtree or lineage (i.e., the --subtree option was not used). The scores were computed by performing a likelihood ratio test at each alignment column (--method LRT), and scores for both conservation and acceleration were produced (--mode CONACC).
The conserved elements were predicted by running phastCons with the --viterbi option. The predicted elements are segments of the alignment that are likely to have been "generated" by the conserved state of the phylo-HMM. Each element is assigned a log-odds score equal to its log probability under the conserved model minus its log probability under the non-conserved model. The "score" field associated with this track contains transformed log-odds scores, taking values between 0 and 1000. (The scores are transformed using a monotonic function of the form a * log(x) + b.) The raw log odds scores are retained in the "name" field and can be seen on the details page or in the browser when the track's display mode is set to "pack" or "full".
This track was created using the following programs:
The phylogenetic tree is based on Murphy et al. (2001) and general consensus in the vertebrate phylogeny community as of March 2007.
Felsenstein J, Churchill GA. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol. 1996 Jan;13(1):93-104. PMID: 8583911
Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21. PMID: 19858363; PMC: PMC2798823
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. PMID: 16024819; PMC: PMC1182216
Siepel A, Haussler D. Phylogenetic Hidden Markov Models. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351.
Yang Z. A space-time process model for the evolution of DNA sequences. Genetics. 1995 Feb;139(2):993-1005. PMID: 7713447; PMC: PMC1206396
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
Harris RS. Improved pairwise alignment of genomic DNA. Ph.D. Thesis. Pennsylvania State University, USA. 2007.
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
Bernard G, Ragan MA, Chan CX. Recapitulating phylogenies using k-mers: from trees to networks. F1000Res. 2016;5:2789. PMID: 28105314
Fan H, Ives AR, Surget-Groba Y, Cannon CH. An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data. BMC Genomics. 2015;16(1):522. PMID: 26169061
Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, Springer MS. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science. 2001 Dec 14;294(5550):2348-51. PMID: 11743200