CAARD:Alpharetroviridae

Revision as of 12:04, 8 May 2009 by imported>Gydbwiki (New page: {{CAARD |pin_output= (RSV:0.363657,LPDV:0.717462,EAV-HP:0.238126); |fin_output= <table class="tabdata"> <tr class="grey"> <td>Name</td> <td>Father</td> <td>Distance to father</td> <td>So...)
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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

(RSV:0.363657,LPDV:0.717462,EAV-HP:0.238126);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name Father Distance to father Sons
RSVN10.363657-
LPDVN10.717462-
EAV-HPN10.238126-
N1root!-RSV LPDV EAV-HP

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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
00.00117484220.0358256440.000505241660.0164059
10.01426230.00166365450.000823669672.37143e-006
20.00273671240.000327972460.00278983680.00531678
30.0318332254.13047e-006470.000254718691.36305e-005
40.0164059260.000117663480.000256299700.000134614
50.01426270.028095490.0116073710.000137404
60.00277929280.0052105500.000433897720.000673734
70.0110915295.31937e-007510.0142713730.0396324
80.00277929300.0318332520.00491497740.0318332
90.00176035310.00277929530.049833750.0142713
100.00014966320.0318332540.0296955760.00491497
110.0193496330.0318332550.000472403773.15422e-006
121.12642e-005344.8452e-005560.0193496780.0396324
139.37352e-005350.0005937570.00414389790.00107153
140.0094486360.000377385580.000356308800.0107323
150.0199208371.57754e-005592.26491e-005811.30637e-005
165.93246e-005380.000935726600.000713136820.000166897
175.23323e-005390.00202355610.00371725830.000360101
180.0094486400.0115495621.21437e-005846.35115e-005
190.0199208417.47892e-006630.0199208850.0283661
200.00123063421.1048e-005645.57873e-006860.00371725
210.0015665436.40288e-006650.00531678  
Total log likelihood of joint reconstruction: -597.807

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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="alpharetroviridae" 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
00.00146915220.0365767440.000964977660.0165011
10.0143427230.00173393450.000887219679.4539e-006
20.00289206240.000692302460.00491213680.0057405
30.0318478259.59089e-006470.000275119693.00893e-005
40.0165011260.000159815480.000269403700.000136978
50.0143427270.040752490.0117445710.00032452
60.00358495280.00556649500.000447465720.000898795
70.0111468291.67886e-006510.0143203730.039697
80.00358495300.0318478520.00517398740.0318478
90.00276598310.00358495530.0501146750.0143203
100.00025867320.0318478540.0306957760.00517398
110.019458330.0318478550.000481192776.45175e-006
122.20432e-005347.13023e-005560.019458780.039697
130.000195066350.000658171570.00687743790.001706
140.00944862360.000385085580.000361199800.0107464
150.0199288373.49291e-005598.37657e-005812.53568e-005
168.00944e-005380.000953747600.000722594820.000852876
178.66336e-005390.00237517610.00381902830.000364597
180.00944862400.0116398623.05705e-005840.000146116
190.0199288412.20451e-005630.0199288850.0288485
200.00139821421.58606e-005641.05485e-005860.00381902
210.00272833431.10597e-005650.0057405  
Total log likelihood of joint reconstruction: -572.891

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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="alpharetroviridae" 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_alpharetroviridae profile HMM generated consensus sequence [hmmemit]
LDsGADvTvisEtdWPssWPaiEasqsqieGvGGatpsrrSenlvqagvInRdGSlEkp
illtPlvAavrgtiLGRdaLrQihgvRl

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

         domain 1 of 1, from 1 to 87: score 40.7, E = 5.7e-13

  DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                      +D+GA+v +vis    + + ++                     s+P 
  AP_alphare     1    LDSGADV-TVIS----ETD-WPS--------------------SWPA 21   

                   sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                    ++s   q++i g+gG ++++  +++ ++q          ++ ++G++  
  AP_alphare    22 IEAS---QSQIEGVGGATPSR--RSENLVQ--------AGVINRDGSL-- 56   

                   venrsl.psdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                      +++ + +  +lv+   +        ILGr d Lrq ++  ++l   
  AP_alphare    57 ---EKPiLLT--PLVA-AVR-----G-TILGR-DALRQIHG--VRL    87   

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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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