CAARD:NIX

Revision as of 10:11, 8 May 2009 by imported>Gydbwiki (New page: {{CAARD |pin_output= (NIXMm:0.022522,NIXh3:0.056116,(NIXrn:0.019703,(NIXm:0.099440,NIXh:0.063818)N3:0.783648)N2:0.014616); |fin_output= <table class="tabdata"> <tr class="grey"> <td>Name...)
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Welcome to the CAARD
The Clan AA Reference Database (CAARD), an in-progress database developed to investigate the major consensus and the phylogeny of clan AA to typify the different protein families according to prior (and further) estimations of their relationships using phylogenies, ancestral reconstructions, sequence logos and HMMs.

Ancestral Maximum Likelihood (ML) Joint Reconstruction

Comments

Ancestral ML reconstructions were performed using FastML 2.02 (Pupko et al. 2000). The tool generates six outputs:

  • Pin; reconstructed ancestral NJ tree in newick format.
  • Fin; parental relationship among reconstructed nodes and contemporary sequences.
  • Jrof; multiple alignment of contemporary sequences and nodes reconstructed with the Joint method.
  • Jpf; joint probability per position and total log likelihood.
  • Mrof; multiple alignment of contemporary sequences and nodes reconstructed with the marginal method
  • Mpf; marginal probability and total log likelihood

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Pin output : Ancestral tree

(NIXMm:0.022522,NIXh3:0.056116,(NIXrn:0.019703,(NIXm:0.099440,NIXh:0.063818)N3:0.783648)N2:0.014616);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name Father Distance to father Sons
NIXMmN10.0225224-
NIXh3N10.0561161-
NIXrnN20.0197031-
NIXmN30.0994395-
NIXhN30.0638182-
N1root!-NIXMm NIXh3 N2
N2N10.0146158NIXrn N3
N3N20.783648NIXm NIXh

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Jpf output: Joint probability per amino acid position and total Log Likelihood

Position Joint probability Position Joint probability Position Joint probability Position Joint probability
00.0202733270.000975997540.000741882810.0469483
10.0185284287.95646e-006550.000462605820.0239413
20.0155666292.47015e-005560.00088901830.0109203
30.0375775300.0375775570.00442840.000163275
40.00030853310.00704066581.68968e-005850.0195498
55.30978e-005327.47067e-006590.0109203860.0144354
65.60797e-007330.00144328604.47274e-006870.00428393
70.0117275340.00309408610.0224882880.0185284
81.14307e-005353.8607e-006620.000824152890.000625625
90.0159245360.024009630.0202733900.00104718
100.0166649370.0009179640.0202733910.000122076
111.60078e-005380.000322545650.0185284920.00201443
120.00371798390.052318662.64657e-005930.00442
130.0109203400.0276989679.04559e-005941.08434e-005
140.00454267410.000350537680.000890541951.86799e-006
156.36957e-006420.0202733690.000557693960.000539514
160.018514430.002392701.10523e-005970.0239413
170.0469483440.0140227710.0038335980.00523597
180.0375775450.00441014720.000994813990.000350906
190.0469483460.0245096730.04694831000.000114797
201.41501e-007470.000536866740.03757751010.000890541
212.28226e-005482.18948e-005750.04694831020.0245096
220.00117634497.38691e-007760.01402271030.00441014
230.0202733500.0195498770.01556661040.024009
240.0276989510.0193248780.04694831050.0208619
251.86201e-005520.000238026790.0009063781060.00454267
260.000543065530.0375775800.01666491070.000484787
Total log likelihood of joint reconstruction: -700.83

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Jrof output: Ancestral ML Reconstruction Alignment

There are two methods of ancestral reconstruction - Joint and Marginal. In this section, we provide a multiple alignment including both input peptidases and ancestral ML sequences reconstructed using the Joint method.The alignment is available in several formats clicking below the option "Set 1". To build HMM profiles and MRC sequences we removed non-informative amino acid stretches and gaps from several ancestral ML reconstruction analyses You can also retrieve the processed Jrof output, clicking below the option "Set 2". Note however that should you cannot select option 2 is because the output was not processed. <align id="nix" folder="jrof"></align>

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Mpf output: Marginal probability per amino acid position and total Log Likelihood

Position Joint probability Position Joint probability Position Joint probability Position Joint probability
00.0202962270.000978563540.000742743810.0469547
10.0185373281.50001e-005550.000463535820.023948
20.0155725294.76717e-005560.000890824830.0109203
30.037579300.037579570.0044369840.000163341
40.000309381310.00706652582.97644e-005850.0466031
55.3114e-005321.28732e-005590.0109203860.0369186
68.93113e-007330.00144739604.5053e-006870.00429769
70.01173340.00309743610.0224983880.0185373
82.33001e-005356.82112e-006620.000824988890.000626462
90.0159398360.0240098630.0202962900.00339208
100.0166744370.000918566640.0202962910.00012801
111.60643e-005380.000323241650.0185373920.00201622
120.00372211390.0852464663.49186e-005930.0044369
130.0109203400.053023670.000137674942.12701e-005
140.00455163410.000350905680.000893508951.879e-006
158.97627e-006420.0202962690.000558238960.000540384
160.0185191430.00239681701.1168e-005970.023948
170.0469547440.0140241710.00383708980.00525373
180.037579450.0044191720.000995167990.000351299
190.0469547460.0245212730.04695471000.000114917
202.80898e-007470.000537363740.0375791010.000893508
212.30876e-005482.59912e-005750.04695471020.0245212
220.0011784491.80935e-006760.01402411030.0044191
230.0202962500.0466031770.01557251040.0240098
240.053023510.0503953780.04695471050.0208631
252.80854e-005520.000553225790.0009072271060.00455163
260.000544716530.037579800.01667441070.000485274
Total log likelihood of joint reconstruction: -685.191

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Mrof output: Ancestral ML Reconstruction Alignment

There are two methods of ancestral reconstruction - Joint and Marginal. In this section, we provide a multiple alignment including both input peptidases and ancestral ML sequences reconstructed using the Joint method.The alignment is available in several formats clicking below the option "Set 1". To build HMM profiles and MRC sequences we removed non-informative amino acid stretches and gaps from several ancestral ML reconstruction analyses You can also retrieve the processed Jrof output, clicking below the option "Set 2". Note however that should you cannot select option 2 is because the output was not processed. <align id="nix" folder="mrof"></align>

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Models

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Sequence logo constructed from the input of the processed Jrof alignment. In every position, each residue is a letter whose height is proportional to its frequency multiplied by the information content of each position measured in bits. Letters are placed such that the most common is at the top.

  • Basic residues are represented in red
  • Hydrophobic residues in black
  • Amino acids frequent in β-turns (G and P) in dark grey
  • Small nucleophiles in violet
  • Acidic residues in orange
  • Acidic-relative amides in green

The logo was constructed using ChekAlign server with the Shannon's algorithm (Shannon 1997) and options "include gaps" and "Correction factor". Gaps are not represented by any symbol but occupy a blank also proportional to its frequency and, for aesthetic reasons, always at the top. Maximum entropy is log221. The alignment gap is considered to be another state or amino acid species.

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HMMs

>AP_nix profile HMM generated consensus sequence
VDTGtqyNlISaaCldRLGLkkrVKskkheGdklslPrtLKvVeQlElllITvGservd
CsAaVVDdnekelsLGLQTLlSLKCiINlDkehrvlrlKadkeElPFle

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Pairwise alignment between the MRC sequence and the DTG/ILG template HMM-profile

        Domain 1 of 1, from 1 to 88: score 28.2, E = 3.3e-09

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    vDTG++  ++is+ c  +++lg                         
AP_nix         1    VDTGTQY-NLISAAC--LDRLG-----------------------L- 20   

                 sktsttaqdtirgagGqskiyvSklktsgqirkn..llslvtikitkGnv
                 +k+ +      + + G+ k       +++++ k+ ++l+l+ i +  G  
AP_nix        21 KKRVK-----SKKHEGD-KL------SLPRTLKVveQLELLLITV--G-- 54   

                 TevenrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                     +++  ++    vv+d e      ++ LG+ + L  l++  i l   
AP_nix        55 ----SERVDCS--AAVVDDNE-----KELSLGL-QTLLSLKCI-INL    88   

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Cite this site

Llorens, C. Futami, R. Renaud, G. and A. Moya (2009). Bioinformatic Flowchart and Database to Investigate the Diversity of Clan AA Peptidases.Biology Direct, 4:3.




Welcome to the Gypsy Database (GyDB) an open editable database about the evolutionary relationship of viruses, mobile genetic elements (MGEs) and the genomic repeats where we invite all authors to contribute with their knowledge to improve and expand the topics.
Cite this project:

Llorens, C., Futami, R., Covelli, L., Dominguez-Escriba, L., Viu, J.M., Tamarit, D., Aguilar-Rodriguez, J. Vicente-Ripolles, M., Fuster, G., Bernet, G.P., Maumus, F., Munoz-Pomer, A., Sempere, J.M., LaTorre, A., Moya, A. (2011) The Gypsy Database (GyDB) of Mobile Genetic Elements: Release 2.0 Nucleic Acids Research (NARESE) 39 (suppl 1): D70-D74 doi: 10.1093/nar/gkq1061

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