CAARD:Errantiviridae

Revision as of 14:04, 8 May 2009 by imported>Gydbwiki (New page: {{CAARD |pin_output= (((HMS-Beagle:0.330354,Yoyo:0.297553)N2:0.168252,(((17.6:0.271949,(297:0.251767,Tom:0.225220)N6:0.147499)N5:0.059692, (Tv1:0.398768,Idefix:0.339277)N7:0.048622)N4:0.40...)
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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

(((HMS-Beagle:0.330354,Yoyo:0.297553)N2:0.168252,(((17.6:0.271949,(297:0.251767,Tom:0.225220)N6:0.147499)N5:0.059692, (Tv1:0.398768,Idefix:0.339277)N7:0.048622)N4:0.405904,(Ted:0.408362,Zam:0.561082)N8:0.129785)N3:0.168457,(Nomad:0.459431, (Burdock:0.215663,(Springer:0.239440,(Gypsyvir:0.176204,Gypsy:0.169050)N12:0.145405)N11:0.058741)N10:0.151782)N9:0.046488);

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Fin output: Parental relationship among reconstructed nodes and OTUs

Show/Hide
Name Father Distance to father Sons
HMS-BeagleN20.330354-
YoyoN20.297553-
17.6N50.271949-
297N60.251767-
TomN60.22522-
Tv1N70.398768-
IdefixN70.339277-
TedN80.408362-
ZamN80.561082-
NomadN90.459431-
BurdockN100.215663-
SpringerN110.23944-
GypsyvirN120.176204-
GypsyN120.16905-
N1root!-N2 N3 N9
N2N10.168252HMS-Beagle Yoyo
N3N10.168457N4 N8
N4N30.405904N5 N7
N5N40.05969217.6 N6
N6N50.147499297 Tom
N7N40.048622Tv1 Idefix
N8N30.129785Ted Zam
N9N10.0464883Nomad N10
N10N90.151782Burdock N11
N11N100.058741Springer N12
N12N110.145405Gypsyvir Gypsy

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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
02.73491e-006262.20859e-016524.12105e-012780.00944641
10.000141637275.5953e-017537.42747e-006793.65488e-005
22.92433e-005285.47157e-009546.83881e-013807.78321e-014
32.00053e-005290.00554974553.23326e-017811.39678e-013
44.82705e-008301.06009e-012561.26219e-016823.19738e-008
51.76965e-010317.205e-017573.40362e-008837.48363e-005
67.19523e-010328.74879e-010581.28019e-014841.52091e-007
78.55598e-008331.18952e-020593.59545e-015856.99411e-014
86.11396e-012341.04749e-009601.03812e-011861.04491e-005
92.92e-010350.00617331614.01989e-009872.23165e-009
102.04326e-018361.99809e-013620.000213424880.00172442
113.13861e-012376.05687e-012632.55562e-016891.23558e-015
121.58675e-015380.000124896642.34014e-018901.26423e-007
132.32747e-010390.00351219659.16777e-024914.44034e-012
140.00658405.56938e-015669.22309e-019925.88021e-005
152.10189e-019412.68086e-007676.41585e-021931.11737e-013
165.16281e-016420.000804845684.84037e-018949.37417e-016
172.50078e-017430.00879857694.23806e-006957.43669e-015
181.27177e-011444.95927e-013700.0106926961.10372e-016
191.48158e-010456.65318e-012710.0258576970.00558862
201.59814e-015463.71894e-007723.15546e-005984.29279e-009
211.89532e-013479.89133e-014733.06932e-005991.7233e-016
228.67425e-019484.76685e-006742.86263e-0131002.87365e-007
238.79362e-006497.88021e-017751.29266e-0091011.15411e-014
241.19392e-005509.47419e-005764.62829e-0111027.87207e-011
251.42475e-017515.75809e-016771.65233e-020  
Total log likelihood of joint reconstruction: -2433.38

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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="errantiviridae3" 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
02.87274e-006269.12321e-016521.09761e-011780.058676
10.000142921271.69004e-016539.00845e-005793.85878e-005
22.94429e-005288.00653e-008542.13425e-012802.0354e-013
32.03323e-005290.058565552.66264e-015815.03438e-013
41.33302e-007301.9785e-012561.02019e-015827.95216e-008
54.17371e-010311.07869e-015571.15428e-007837.62803e-005
61.23558e-009323.18943e-009583.4691e-013841.61364e-007
71.65518e-007331.08699e-019593.24599e-014851.28105e-013
82.04006e-011342.53163e-009606.14257e-011861.17027e-005
94.40765e-010350.076748611.08979e-007872.8583e-009
102.15072e-017364.06744e-013620.000561817880.00172555
115.42116e-012371.40157e-011633.14475e-016897.61517e-015
129.36008e-015380.000126504641.12392e-017901.43029e-007
135.81735e-009390.042645651.11673e-022911.10078e-011
140.066005403.47183e-014667.51499e-018926.17812e-005
151.60065e-018418.9673e-007675.57004e-019933.75948e-013
166.95682e-015420.0103865681.42412e-017943.00992e-015
171.73244e-016430.0345596696.64938e-005951.16281e-014
181.92441e-011441.58275e-012700.058676964.21128e-016
196.49989e-009451.10513e-011710.091904970.040752
205.45467e-015462.08709e-005723.17935e-005989.56084e-009
219.51639e-013471.59945e-012739.47168e-005991.36285e-015
222.49386e-017483.67835e-005747.40621e-0131003.9867e-007
230.000206364491.89877e-016752.62746e-0091014.26779e-014
240.000169346500.00138433765.21358e-0111029.76675e-011
253.76171e-017514.80593e-015773.00597e-019  
Total log likelihood of joint reconstruction: -2282.45

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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="errantiviridae3" 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_errantiviridae profile HMM generated consensus sequence
IDTGSnkNyIrpnllklpvqntfsVttihGitlkrslnipskfntteqFFlLhslssyF
DglIGrdlLkqaeAkidl

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

        Domain 1 of 1, from 1 to 77: score 43.4, E = 8.7e-14

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    +DTG++  + i ++   ++kl                        P 
AP_erranti     1    IDTGSNK-NYIRPN---LLKL------------------------PV 19   

                 sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                 ++t+      +++++G++ +     +++          +  k +      
AP_erranti    20 QNTFS-----VTTIHGITLK-----RSLN---------IPSKFN-T---- 45   

                 venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                       +++  f+++++++    ++d+++Gr d+L+q++++ idl   
AP_erranti    46 ------TEQ--FFLLHSLSS---YFDGLIGR-DLLKQAEAK-IDL    77   

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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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