CAARD:Del

Revision as of 14:19, 8 May 2009 by imported>Gydbwiki (New page: {{CAARD |pin_output= (Retrosat-2:0.508055,(Del:0.418355,Peabody:0.549836)N2:0.130960,(Tma:0.402571,(Legolas:0.242758,T32022.14:0.203860)N4:0.161988)N3:0.114301); |fin_output= <tab...)
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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

(Retrosat-2:0.508055,(Del:0.418355,Peabody:0.549836)N2:0.130960,(Tma:0.402571,(Legolas:0.242758,T32022.14:0.203860)N4:0.161988)N3:0.114301);

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Fin output: Parental relationship among reconstructed nodes and OTUs

Show/Hide
Name Father Distance to father Sons
Retrosat-2N10.508055-
DelN20.418355-
PeabodyN20.549836-
TmaN30.402571-
LegolasN40.242758-
T32022.14N40.20386-
N1root!-Retrosat-2 N2 N3
N2N10.13096Del Peabody
N3N10.114301Tma N4
N4N30.161988Legolas T32022.14

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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
02.7634e-005231.10388e-008462.95462e-010691.79097e-005
10.00340934244.5987e-005475.46282e-007701.81182e-007
26.51993e-005253.68548e-007482.98556e-008711.97168e-009
30.012882264.72605e-010492.01879e-005721.08361e-009
40.00034288275.28418e-010506.94776e-007730.000331831
50.000247001283.51867e-010512.87177e-010740.000593411
60.00108388291.78104e-011523.42206e-005750.000232902
75.78206e-007303.4521e-010536.62623e-010760.0157214
80.00728457313.18662e-010540.000318662770.012882
90.000215364324.15036e-005553.69214e-008780.000992219
102.55547e-005336.54366e-011560.000116756790.000405409
114.90025e-006343.08845e-007572.46362e-010800.00607546
123.84603e-009359.93104e-006580.000301277810.0157214
132.04605e-011367.75457e-007591.3389e-009824.16937e-008
147.89797e-007370.000278985605.43052e-007831.8179e-009
153.40311e-007388.54457e-007612.43292e-007841.31705e-005
161.02062e-007395.85657e-008621.76841e-007851.49643e-006
173.83996e-006401.325e-006630.000375865862.77732e-006
180.0256058412.83972e-011640.0157214872.46585e-010
191.20809e-005421.64652e-005650.000717642882.13213e-006
208.14809e-008431.80542e-009661.43404e-006891.83085e-005
212.57073e-006442.95731e-007676.58007e-007900.00425104
228.98156e-008450.00917882684.14629e-007  
Total log likelihood of joint reconstruction: -1216.83

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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="del" 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
03.58e-005234.47251e-008461.71163e-009691.84782e-005
10.00342907244.98009e-005472.24501e-006701.96813e-007
20.000118185253.8085e-007486.66948e-008711.34856e-008
30.0128872261.31548e-009492.14938e-005726.23089e-009
40.000368313272.51826e-009501.1961e-006730.000363925
50.000252836283.56181e-009515.11957e-010740.000686706
60.00108462291.76943e-010525.39671e-005750.000249252
71.14753e-006302.1816e-009531.53843e-009760.0157456
80.00728899311.59924e-009540.000350446770.0128872
90.00031009324.28742e-005552.98826e-007780.000992838
103.22474e-005335.4568e-010560.000117233790.000418738
114.99118e-006348.69656e-007571.5566e-009800.00607547
129.63833e-009351.7958e-005580.00132329810.0157456
132.63661e-010361.59509e-006594.25748e-009821.44756e-007
141.2906e-006370.000280208601.05817e-006835.82169e-009
154.9634e-007381.45689e-006616.01537e-007841.34158e-005
161.12732e-007391.19974e-007625.27854e-007854.19233e-006
172.3916e-005402.84404e-006630.000382615864.07863e-006
180.058676412.06724e-010640.0157456875.64738e-010
191.40461e-005421.84375e-005650.000772417884.05002e-006
203.30395e-007433.51732e-009661.61425e-006892.0148e-005
213.16396e-006447.55317e-007672.26968e-006900.00425114
222.31437e-007450.0163371684.68957e-007  
Total log likelihood of joint reconstruction: -1154.91

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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="del" folder="mrof"></align>

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Models

Logo del.png

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_del profile HMM generated consensus sequence
fDsGATHsFISpemvgkmgeirkeplgdpgvVnaAgGsstsvtgSvvkgvpisInGrem
paDLIilpledhDVILGMDWLakYrvvlDC

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

       Domain 1 of 1, from 1 to 89: score 77.0, E = 6.8e-24

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    +D+GA++ s+is+e  ++ k+g+ rk                  +P+
AP_del         1    FDSGATH-SFISPE--MVGKMGEIRK------------------EPL 26   

                 sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                  ++++     + +agG+s +      ++g++ k+    v i+i+ G    
AP_del        27 GDPGV-----VNAAGGSSTS------VTGSVVKG----VPISIN-G---- 56   

                 venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                    r++p d    ++ ++ed     dvILG+ d+L ++  v  d+   
AP_del        57 ---REMPAD--LIIL-PLED----HDVILGM-DWLAKYRVV-LDC    89   

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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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