CAARD:TF1-2

Revision as of 13:38, 8 May 2009 by imported>Gydbwiki (New page: {{CAARD |pin_output= (N1:0.0,TF2:0.300000); |fin_output= <table class="tabdata"> <tr class="grey"> <td>Name</td> <td>Father</td> <td>Distance to father</td> <td>Sons</td> </tr> <...)
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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

(N1:0.0,TF2:0.300000);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name Father Distance to father Sons
TF2N10.3-
TF1N10.3-
N1root!-TF2 TF1

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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
00.0259827210.0269084420.0269084630.0347441
10.028196220.0283934430.0011932640.0275402
20.0269084230.0330756440.0347441650.0297219
30.0498761240.0118237450.0621819660.0117064
40.0372241250.000631961460.000193889670.0330756
50.0220105260.00124806470.0259827680.0372241
60.00230045270.0297219480.00210886690.0372241
70.0201276280.032548490.0621819700.0259827
80.00496762290.0259827500.0201276710.0297219
90.0259827300.0224481510.0498761720.0275402
100.0269084310.0498761520.0259827730.0269084
110.0358474320.0498761530.0297219740.0269084
120.0358474330.032548540.0259827750.0621819
130.0269084340.0224481550.0347441760.0224481
140.032548350.0330756560.0269084770.028196
150.0283934360.000934252570.0358474780.0201276
160.0372241370.0347441580.0275402790.0201276
170.0117064380.0259827590.0621819800.0259827
180.0347441390.0201276600.032548810.0358474
190.0621819400.0283934610.032548820.0259827
200.0330756410.0347441620.0347441  
Total log likelihood of joint reconstruction: -316.641

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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="tf1_2" 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
00.0269992210.0276271420.0276271630.0353273
10.028886220.0288953430.00263986640.0277081
20.0276271230.0332631440.0353273650.0307625
30.050169240.0118267450.0628339660.0118167
40.0382672250.00170555460.000508665670.0332631
50.0222665260.00278997470.0269992680.0382672
60.0049056270.0307625480.00437808690.0382672
70.0205182280.0338425490.0628339700.0269992
80.0102288290.0269992500.0205182710.0307625
90.0269992300.0225776510.050169720.0277081
100.0276271310.050169520.0269992730.0276271
110.0366289320.050169530.0307625740.0276271
120.0366289330.0338425540.0269992750.0628339
130.0276271340.0225776550.0353273760.0225776
140.0338425350.0332631560.0276271770.028886
150.0288953360.00216192570.0366289780.0205182
160.0382672370.0353273580.0277081790.0205182
170.0118167380.0269992590.0628339800.0269992
180.0353273390.0205182600.0338425810.0366289
190.0628339400.0288953610.0338425820.0269992
200.0332631410.0353273620.0353273  
Total log likelihood of joint reconstruction: -308.435

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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="tf1_2" 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_TF profile HMM generated consensus sequence
iDtGAqvniitEEtvRAHKLPtRPWsqsviYGGvYPnKinRKtiKLninLnGisiKtEF
LvvKKFsHPAAisFttLYDnniEi

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

        Domain 1 of 1, from 1 to 83: score 43.4, E = 8.5e-14

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    +DTGA+v ++i++e++ a kl+                     ++P+
AP_TF          1    IDTGAQV-NIITEETVRAHKLP---------------------TRPW 25   

                 sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                 s +s      + + gG ++      k++ +++k     + i ++ G    
AP_TF         26 S-QS------V-IYGGVYPN-----KINRKTIK-----LNINLN-G---- 52   

                 venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                     s++++  flvv         + +   +  f + +  + i++   
AP_TF         53 ---ISIKTE--FLVV-KK------FSHPAAI-SFTTLYDNN-IEI    83   

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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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