CAARD:412 mdg1

Revision as of 13:28, 8 May 2009 by imported>Gydbwiki (New page: {{CAARD |pin_output= (N1:0.0,412:0.300000); |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

(N1:0.0,412:0.300000);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name Father Distance to father Sons
412N10.3-
Mdg1N10.3-
N1root!-412 Mdg1

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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
00.00197082220.000673976440.0358474660.0330756
10.028196230.0201276450.000992501670.000204135
20.0269084240.000673976462.74472e-005680.028196
30.0498761250.0011932470.0011932690.0498761
40.0372241260.0201276480.00202552700.0259827
50.00405512270.0259827490.00102642710.0259827
60.0259827280.000314974508.54331e-005720.0498761
70.0297219290.0498761510.00230045730.00197082
80.00197082300.0259827520.0259827740.028196
90.0621819310.0498761530.0330756750.0275402
100.0347441320.0220105540.000702156760.0259827
112.38116e-005330.000196896550.00405512770.0347441
120.000248302340.000673976560.0275402780.0347441
130.00210886350.0259827570.0117064790.0224481
140.00173055360.0220105580.00197082800.0201276
150.00102642370.0297219590.032548810.0141207
160.00189948380.000364737600.000113966826.52615e-005
170.00210886390.0498761610.00102642830.00197082
180.00173055400.000253439620.0201276840.00405512
190.00197082410.000342861630.0275402850.00189948
200.00030487428.97346e-005640.0330756  
210.000108934430.00197082650.0259827  
Total log likelihood of joint reconstruction: -465.369

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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="412_mdg1" 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
00.00479559220.00148284440.0366289660.0332631
10.028886230.0205182450.00219789670.000453979
20.0276271240.00148284468.03607e-005680.028886
30.050169250.00263986470.00263986690.050169
40.0382672260.0205182480.00406281700.0269992
50.0083426270.0269992490.00232551710.0269992
60.0269992280.000818564500.00023484720.050169
70.0307625290.050169510.0049056730.00479559
80.00479559300.0269992520.0269992740.028886
90.0628339310.050169530.0332631750.0277081
100.0353273320.0222665540.00154784760.0269992
117.35313e-005330.00057839550.0083426770.0353273
120.000767354340.00148284560.0277081780.0353273
130.00437808350.0269992570.0118167790.0225776
140.00373254360.0222665580.00479559800.0205182
150.00232551370.0307625590.0338425810.0141382
160.0038781380.000908252600.000321467820.000217822
170.00437808390.050169610.00232551830.00479559
180.00373254400.000652718620.0205182840.0083426
190.00479559410.00111944630.0277081850.0038781
200.000765612420.000265058640.0332631  
210.000346017430.00479559650.0269992  
Total log likelihood of joint reconstruction: -426.644

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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="412_mdg1" 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_412_mdg1 profile HMM generated consensus sequence
iDtGAdisiLKcnnnnlnniqpknkiniqGiGqqkiqsrGqthiEmcignyviPhdFHi
vpnnFPiPcDGiiGiDFiKKYnCqidf

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

         domain 1 of 1, from 1 to 86: score 73.1, E = 9.6e-23

  DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                      +DTGA++ s+++++  + + l                       qP+
  AP_412_mdg     1    IDTGADI-SILKCN--NNN-LNN--------------------IQPK 23   

                   sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                   +k++      i+g+ Gq+ki     ++ gq++      ++ +i  G    
  AP_412_mdg    24 NKIN------IQGI-GQQKI-----QSRGQTH------IEMCI--G---- 49   

                   venrslpsdgvflvv.tdpedqksrydvILGrldfLrqlnsvhidl<-*
                     n+ +p+d  f++v+ +  +   ++d+I+G+ df +++n+  id+   
  AP_412_mdg    50 --NYVIPHD--FHIVpNNFPI---PCDGIIGI-DFIKKYNCQ-IDF    86   

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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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