CAARD:Lentiviridae

Revision as of 11:53, 8 May 2009 by imported>Gydbwiki (New page: {{CAARD |pin_output= (HIV-1:0.240948,(HIV-2:0.242190,SIVMAC:0.024963)N2:0.322066,((SIVMND:0.195084,SIVAGM:0.255789)N4:0.105710,(EIAV:0.495777, (BIV:0.687844,(FIV:0.535661,(VMV:0.195681,(SA...)
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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

(HIV-1:0.240948,(HIV-2:0.242190,SIVMAC:0.024963)N2:0.322066,((SIVMND:0.195084,SIVAGM:0.255789)N4:0.105710,(EIAV:0.495777, (BIV:0.687844,(FIV:0.535661,(VMV:0.195681,(SA-OMVV:0.130900,CAEV:0.176330)N9:0.030231)N8:0.233957)N7:0.158380)N6:0.032682) N5:0.209928)N3:0.023193);

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Fin output: Parental relationship among reconstructed nodes and OTUs

Show/Hide
Name Father Distance to father Sons
HIV-1N10.240948-
HIV-2N20.24219-
SIVMACN20.0249634-
SIVMNDN40.195084-
SIVAGMN40.255789-
EIAVN50.495777-
BIVN60.687844-
FIVN70.535661-
VMVN80.195681-
SA-OMVVN90.1309-
CAEVN90.17633-
N1root!-HIV-1 N2 N3
N2N10.322066HIV-2 SIVMAC
N3N10.0231928N4 N5
N4N30.10571SIVMND SIVAGM
N5N30.209928EIAV N6
N6N50.0326816BIV N7
N7N60.15838FIV N8
N8N70.233957VMV N9
N9N80.0302306SA-OMVV CAEV

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

<tbody>
Position Joint probability Position Joint probability Position Joint probability Position Joint probability
05.7476e-008260.00731698524.45852e-008788.27202e-007
10.000710229272.88386e-013531.59508e-010790.000130151
20.000232626283.81371e-014541.8688e-010801.90035e-006
30.00475041291.31587e-007551.64464e-010818.33775e-010
42.20693e-005302.1178e-006562.76006e-010820.0155517
50.000710229312.55684e-005570.00996842831.53987e-006
68.43787e-012322.04917e-013580.00983769841.3617e-008
74.39935e-007336.14377e-010590.0138407850.00475041
86.49805e-006342.50307e-009605.9434e-009860.000726912
92.63725e-009350.00475041612.02065e-010871.26968e-006
109.04494e-011361.43748e-005621.23648e-012882.2475e-005
115.71143e-005370.000148363633.92614e-011893.06924e-008
121.79819e-008380.0255148649.68696e-006904.24072e-013
132.76373e-015390.00475041650.000626357917.79496e-010
145.75746e-018400.00818183662.01639e-015921.22635e-016
155.49705e-012410.00454973671.69588e-015931.4552e-008
168.4979e-006425.56131e-013681.40002e-019942.65282e-008
172.01314e-008432.36297e-009691.10253e-006951.11407e-010
189.18525e-007447.30644e-011704.72957e-009964.76167e-014
193.99302e-018452.49677e-009714.79102e-009973.78883e-005
200.0110107466.64372e-009721.86631e-008981.32658e-007
212.7288e-010472.00451e-010732.5724e-007992.59205e-007
229.5127e-005486.00519e-008745.43415e-0101002.24605e-010
233.72236e-016491.37822e-011751.55809e-0131011.17443e-010
244.24771e-007504.20091e-012762.18557e-0121023.52152e-007
250.00688408510.0101504772.8037e-008  
Total log likelihood of joint reconstruction: -1821.38

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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="lentiviridae" 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
07.69272e-008260.053761525.02644e-008781.22621e-006
10.000713303277.88163e-013534.47837e-010790.000130797
20.000233367282.34587e-013545.02691e-010804.77703e-006
30.00475182291.46327e-007551.90883e-010812.26444e-009
42.23371e-005303.37457e-006563.00782e-010820.050901
50.000713303310.000155734570.051691833.26661e-006
68.87235e-011328.45748e-013580.051544841.81405e-008
74.61081e-007332.56055e-009590.06183850.00475182
88.17732e-006343.69355e-009604.57111e-008860.000728644
94.40838e-009350.00475182615.06531e-009871.86041e-006
107.87715e-010362.22885e-005622.32358e-012880.00015284
110.000397964370.000148594634.58417e-011894.57224e-008
121.47718e-007380.073152641.52245e-005901.15574e-012
139.62944e-015390.00475182650.00297462911.16483e-008
142.05723e-017400.066005664.26744e-015923.55837e-016
151.04797e-011410.042645675.11101e-015931.5565e-008
163.93375e-005424.39219e-012682.18894e-018942.70342e-008
173.12146e-007432.898e-009691.1086e-006954.74787e-010
187.34618e-006443.89735e-010704.97747e-009969.87387e-014
195.22933e-017455.91622e-009712.68439e-008977.10306e-005
200.032102461.38758e-008729.93937e-008983.65841e-007
211.30578e-009479.61301e-010736.89278e-007994.53404e-007
229.57315e-005486.16114e-008741.73143e-0091003.02339e-010
236.40125e-016491.76135e-011752.94412e-0131012.74145e-010
242.66435e-006505.11916e-012762.76138e-0121023.76939e-007
250.068765510.053761772.15765e-007  
Total log likelihood of joint reconstruction: -1720.76

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

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Models

Logo lentiviridae.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_lentiviridae profile HMM generated consensus sequence [hmmemit]
LDTGADdtIlkthrdlklpGkpkgkiiiGIGGiikvkkydnVhveikykgkriiGtvvv
vapdtPvnilGRdnmlqkLgirLimaqL

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

          domain 1 of 1, from 1 to 82: score 50.4, E = 6.9e-16

  DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                      +DTGA+  +++++     +kl+                     ++P+
  AP_lentivi     1    LDTGADD-TILKTH--RDLKLP---------------------GKPK 23   

                   sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                    k+       i g+gG+ k+     k++  ++      v+ik + G    
  AP_lentivi    24 GKI-------IIGIGGIIKV-----KKYDNVH------VEIKYK-G---- 50   

                   venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                     +r +++   ++vv  p+     +  ILGr d + q+ +  i+l   
  AP_lentivi    51 --KRIIGT---VVVV-APDT----PVNILGR-DNMLQKLG--IRL    82  

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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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