CAARD:Gammaretroviridae

Revision as of 12:00, 8 May 2009 by imported>Gydbwiki (New page: {{CAARD |pin_output= (FeLV:0.074252,(BAEVM:0.177409,((Herv.E:0.330059,RTVL.H3:0.397258)N4:0.043729,((MdEV:0.117158,(KorV:0.051457,GALV:0.041148)N7:0.023153) N6:0.106950,(PERV.MSL:0.162721,...)
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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

(FeLV:0.074252,(BAEVM:0.177409,((Herv.E:0.330059,RTVL.H3:0.397258)N4:0.043729,((MdEV:0.117158,(KorV:0.051457,GALV:0.041148)N7:0.023153) N6:0.106950,(PERV.MSL:0.162721,(Q88269:0.335537,REV:0.226503)N9:0.044583)N8:0.024222)N5:0.040673)N3:0.035644)N2:0.051896, (CHO.K1:0.122359,MuLV:0.079455)N10:0.006934);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name Father Distance to father Sons
FeLVN10.0742518-
BAEVMN20.177409-
Herv.EN40.330059-
RTVL.H3N40.397258-
MdEVN60.117158-
KorVN70.0514574-
GALVN70.0411484-
PERV.MSLN80.162721-
Q88269N90.335537-
REVN90.226503-
CHO.K1N100.122359-
MuLVN100.0794548-
N1root!-FeLV N2 N10
N2N10.0518959BAEVM N3
N3N20.035644N4 N5
N4N30.0437293Herv.E RTVL.H3
N5N30.0406726N6 N8
N6N50.10695MdEV N7
N7N60.0231535KorV GALV
N8N50.0242217PERV.MSL N9
N9N80.044583Q88269 REV
N10N10.00693423CHO.K1 MuLV

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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
07.0903e-006172.06774e-013343.02075e-012510.00843806
10.00409784187.15108e-010351.36025e-009521.14077e-013
20.00225569192.04809e-015361.69932e-016530.00843806
30.000643944202.53548e-012370.000255183540.0179303
40.00369529213.59202e-017381.98331e-008550.0179303
53.18526e-011220.0148059397.03591e-016560.000349375
60.001388236.82992e-006404.92131e-005570.00421309
75.01132e-005241.32317e-008411.83262e-008580.0003562
80.000127597250.0148059420.001388590.000895871
92.04489e-005262.70036e-009432.20665e-005600.0179303
103.71639e-015277.62572e-007440.0083459611.34406e-008
117.06709e-020281.39203e-018450.0179303620.00653438
125.66295e-010291.01238e-010461.58679e-012630.000263054
137.01289e-006309.11851e-013475.15942e-007647.15299e-014
149.60083e-013311.12326e-010480.00843806651.10447e-006
153.14686e-011322.84939e-006492.48944e-008664.75669e-010
162.13334e-015332.47728e-009500.00485142671.62086e-005
Total log likelihood of joint reconstruction: -1116.14

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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="gammaretroviridae" 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
07.51965e-006176.17775e-013345.70703e-012510.00843862
10.00410181181.04178e-009351.42824e-009523.41556e-013
20.00225731196.31039e-015362.37055e-016530.00843862
30.000648327205.65637e-012370.000257423540.0179351
40.00369849214.02912e-016382.76715e-008550.0179351
54.0397e-011220.014807392.1986e-015560.000350442
60.00138817236.99298e-006404.97564e-005570.00421537
75.03437e-005241.44632e-008412.75158e-008580.00035981
80.000129386250.014807420.00138817590.000903306
92.0931e-005261.52431e-008432.23159e-005600.0179351
101.0065e-014271.07891e-006440.0083468613.19135e-008
111.79617e-019283.1275e-018450.0179351620.0065381
126.05901e-010293.30667e-010461.90698e-012630.000264099
137.03905e-006303.63885e-012477.51521e-007642.32844e-013
141.12063e-012311.55851e-010480.00843862651.12541e-006
153.3123e-011323.46562e-006495.77459e-008661.69647e-009
163.80101e-015333.70343e-009500.00485144671.65441e-005
Total log likelihood of joint reconstruction: -1091.89

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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="gammaretroviridae" 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_gammaretroviridae profile HMM generated consensus sequence
vDtgAeHsvltqpplssktaviGatGqkqypwttkvqlgkvtHsFLviPecPlPLLgRd
lLtKLkaqi

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

        Domain 1 of 1, from 1 to 68: score 45.0, E = 2.8e-14

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    vDTGA++ sv++       + +                        s
AP_gammare     1    VDTGAEH-SVLT-------QPP-----------------------LS 16   

                 sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                 skt       + ga Gq+++       +++        +++++  G    
AP_gammare    17 SKTA------VIGATGQKQY-------PWT--------TKVQL--G---- 39   

                 venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                     + +++  flv+  pe+    +  +LGr d+L++l+    ++   
AP_gammare    40 ----KVTHS--FLVI--PEC----PLPLLGR-DLLTKLK---AQI    68   

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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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