Observations on Influenza Viri Phylogony. 02/04/07 Bioinformatics: Hatem Nassrat
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1 Observations on Influenza Viri Phylogony
2 Introduction Influenza Viri Mutation Differences: in sequence structure and protein function between different mutations Likelihood Calculation: to determine the likelihood of a mutation between two different influenza viri proteins
3 Procedure To calculate the likelihood of the mutation, the sequences have to undergo certain computations Influenza Viri protein pairs are generated and searched for within the Influenza database Sequence pairs that have both protein 1 and protein 2, coming from the same strain are placed in Fasta files. Fasta files are aligned using Clustalw The allignments are passed to Phyml for likelihood computation
4 Procedure FLU Find all sequences with protein X, and Y where they appear within the same strain Fasta file seq with X Fasta file seq with Y Fasta File with matching seq concatonated Clustalw Likelihood values For the three computed trees Phyml
5 Input Data Sequences from a group of viri Along with other attributes: Organism from which the strain was sequenced The virus protein found within the sequence A definition of the protein
6 Input Data h_type n_type protein strain definition gi seq H1 N2 PB1 A/duck/NC/91347/01(H1N2) polymerase subunit PB1 [Influenza A virus (A/duck/NC/91347/01(H1N2))] MDVNPTLLF... H1 N2 PB1 A/swine/Cotes d'armor/2433/98(h1n2) polymerase subunit 1 [Influenza A virus (A/swine/Cotes d'armor/2433/98(h1n MDVNPTLLF... H1 N2 PB1 A/swine/Cotes d'armor/604/99(h1n2) polymerase subunit 1 [Influenza A virus (A/swine/Cotes d'armor/604/99(h1n MDVNPTLLF... H1 N2 PB1 A/swine/Cotes d'armor/790/97(h1n2) polymerase subunit 1 [Influenza A virus (A/swine/Cotes d'armor/790/97(h1n MDVNPTLLF... H1 N2 PB1 A/swine/Cotes d'armor/800/00(h1n2) polymerase subunit 1 [Influenza A virus (A/swine/Cotes d'armor/800/00(h1n TLLFLKVPAQNA... H1 N2 PB1 A/swine/Italy/1081/00(H1N2) polymerase subunit 1 [Influenza A virus (A/swine/Italy/1081/00(H1N2))] LLFLKVPAQNAI... H1 N2 PB1 A/swine/Italy/1521/98(H1N2) polymerase subunit 1 [Influenza A virus (A/swine/Italy/1521/98(H1N2))] MDVNPTLLFLK... H1 N2 PB1 A/swine/Italy/2064/99(H1N2) polymerase subunit 1 [Influenza A virus (A/swine/Italy/2064/99(H1N2))] FLKVPAQNAIST.. H1 N2 PB1 A/Swine/Korea/CY02/02(H1N2) polymerase subunit 1 [Influenza A virus (A/Swine/Korea/CY02/02(H1N2))] MDVNPTLLFLK... H1 N2 PB1 A/swine/Ontario/48235/04(H1N2) polymerase subunit PB1 [Influenza A virus (A/swine/Ontario/48235/04(H1N2)) MDVNPTLLFLK... H1 N2 PB1 A/swine/Ontario/52156/03(H1N2) polymerase subunit PB1 [Influenza A virus (A/swine/Ontario/52156/03(H1N2)) MDVNPTLLFLK... H1 N2 PB1 A/swine/Ontario/55383/04(H1N2) polymerase subunit PB1 [Influenza A virus (A/swine/Ontario/55383/04(H1N2)) MDVNPTLLFLK... H1 N2 PB1 A/swine/Scotland/410440/94(H1N2) polymerase subunit 1 [Influenza A virus (A/swine/Scotland/410440/94(H1N2))] MDVNPTLLFLK... H1 N2 PB1 A/swine/Zhejiang/1/2004(H1N2) PB1 [Influenza A virus (A/swine/Zhejiang/1/2004(H1N2))] MDVNPTLLFLK... H1 N2 PB1 A/Yokohama/22/2002(H1N2) polymerase subunit 1 [Influenza A virus (A/Yokohama/22/2002(H1N2))] MDVNPTLLFLK...
7 Hunting Sequences The sequences are in a MySQL database To get the sequences SQL similar to the following is used: SELECT A.*,B.* FROM influenza_a A, influenza_a B WHERE A.strain = B.strain AND A.protein = X AND B.protein = Y AND A.h_type = B.h_type and A.n_type = B.n_type AND A.h_type = H_range and A.n_type = N_range A.* area of result belongs to all applicable seq with protein X Similarly B.* represents protein Y The three Fasta files are generated from this result
8 Alignment The contents of the Fasta files are sent to Clustalw for alignment Clustalw options are set to make the output readable by Phyml (PHYLIB)
9 Phyml A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood The aligned sequences are passed to this algorithm Three likelihood values are computed: Likelihood of seq w/ Protein X (L1) Likelihood of seq w/ Protein Y (L2) Likelihood of concat. seqs w/ Protein X.Y (L12)
10 Likelihood This likelihood is used to compute a measure of the probablity of a mutation between viri with protein X to viri with protein Y Mutation Likelihood = L1 + L2 L12 The closer the number is to zero the easier the mutation between the two viri sequences
11 Experiment and Results The Expirement was setup as described earlier A MySQL db with many influenza viri seqs was used to gather the data A program was written to encapsulate the illustrated procedure and combinatorially find the different proteins and ranges to be searched Likelihood values were calculated and compiled
12 Experiment and Results Many total likelihood values where close to zero while others were quite higher Examples with high values include the proteins PA, NP within the H1/N2 range gi h_type n_type protein strain definition seq H1 N2 PA A/swine/Bakum/1832/00(H1N2) polymerase acidic protein [Influenza A virus (A/swine/Bakum/1832/00(H1N2))]. MKEHGEDPK H1 N2 NP A/swine/Bakum/1832/00(H1N2) nucleoprotein [Influenza A virus (A/swine/Bakum/1832/00(H1N2))]. MVMELIRMIK H1 N2 NP A/duck/NC/91347/01(H1N2) nucleoprotein [Influenza A virus (A/duck/NC/91347/01(H1N2))]. MASQGTKRS H1 N2 PA A/duck/NC/91347/01(H1N2) acidic protein 2 [Influenza A virus (A/duck/NC/91347/01(H1N2))]. MEDFVRQCFN The total likelihood for these two proteins is
13 Experiment and Results Other Findings Proteins PB1, NA (within H1/N2) (lk = ) Gi h_type n_type protein strain definition Seq H1 N2 NA A/swine/Italy/1081/00(H1N2) neuraminidase [Influenza A virus (A/swine/Italy/1081/00(H1N2))]. IITIGSVS H1 N2 PB1 A/swine/Italy/1081/00(H1N2) polymerase subunit 1 [Influenza A virus (A/swine/Italy/1081/00(H1N2))]. LLFLKVPA H1 N2 NA A/swine/Italy/1521/98(H1N2) neuraminidase [Influenza A virus (A/swine/Italy/1521/98(H1N2))]. TIGSVSLS H1 N2 PB1 A/swine/Italy/1521/98(H1N2) polymerase subunit 1 [Influenza A virus (A/swine/Italy/1521/98(H1N2))]. MDVNPTL H1 N2 PB1 A/Swine/Korea/CY02/02(H1N2) polymerase subunit 1 [Influenza A virus (A/Swine/Korea/CY02/02(H1N2))]. MDVNPTL H1 N2 NA A/Swine/Korea/CY02/02(H1N2) neuraminidase [Influenza A virus (A/Swine/Korea/CY02/02(H1N2))]. MNPNQKI... Proteins PB1, NS2 (within H1/N2) (lk = ) Gi h_type n_type protein strain definition Seq H1 N2 NS2 A/duck/NC/91347/01(H1N2) nonstructural protein 2 [Influenza A virus (A/duck/NC/91347/01(H1N2))]. MDSNTVSSFQ H1 N2 PB1 A/duck/NC/91347/01(H1N2) polymerase subunit PB1 [Influenza A virus (A/duck/NC/91347/01(H1N2))]. MDVNPTLLFL H1 N2 PB1 A/duck/NZL/41/1984(H1N2) polymerase PB1 [Influenza A virus (A/duck/NZL/41/1984(H1N2))]. MDVNPTLLFL H1 N2 NS2 A/duck/NZL/41/1984(H1N2) nonstructural protein 2 [Influenza A virus (A/duck/NZL/41/1984(H1N2))]. MDSNTVSSFQ H1 N2 NS2 A/swine/Ontario/55383/04(H1N2) nonstructural protein 2 [Influenza A virus (A/swine/Ontario/55383/04(H1N2))]. MDSNTVSSFQ H1 N2 PB1 A/swine/Ontario/55383/04(H1N2) polymerase subunit PB1 [Influenza A virus (A/swine/Ontario/55383/04(H1N2))]MDVNPTLLFL H1 N2 NS2 A/swine/Scotland/410440/94(H1N2) non structural protein 2 [Influenza A virus (A/swine/Scotland/410440/94(H1N2))MDSNTVSSFQ H1 N2 PB1 A/swine/Scotland/410440/94(H1N2) polymerase subunit 1 [Influenza A virus (A/swine/Scotland/410440/94(H1N2))].MDVNPTLLFL
14 Experiment and Results Proteins PB2, PB1 (within H2/N2) (lk = ) Gi h_type n_type protein strain definition Seq H2 N2 PB2 A/duck/Hong Kong/319/1978(H2N2) polymerase PB2 [Influenza A virus (A/duck/Hong Kong/319/1978(H2N2))]. MERIKELR H2 N2 PB1 A/duck/Hong Kong/319/1978(H2N2) polymerase PB1 [Influenza A virus (A/duck/Hong Kong/319/1978(H2N2))]. MDVNPTLL H2 N2 PB2 A/Canada/720/05(H2N2) PB2 polymerase subunit [Influenza A virus (A/Canada/720/05(H2N2))]. MERIKELR H2 N2 PB1 A/Canada/720/05(H2N2) PB1 polymerase subunit [Influenza A virus (A/Canada/720/05(H2N2))]. MDVNPTLL... Proteins PB2, NP (within H2/N2) (lk = ) Gi h_type n_type protein strain definition Seq H2 N2 PB2 A/duck/Hong Kong/319/1978(H2N2) polymerase PB2 [Influenza A virus (A/duck/Hong Kong/319/1978(H2N2))]. MERIKELRD H2 N2 NP A/duck/Hong Kong/319/1978(H2N2) nucleocapsid protein [Influenza A virus (A/duck/Hong Kong/319/1978(H2N2))]. MASQGTKRS H2 N2 NP A/Georgia/1/67(H2N2) nucleoprotein [Influenza A virus (A/Georgia/1/67(H2N2))]. MASQGTKR H2 N2 PB2 A/Georgia/1/67(H2N2) PB2 polymerase subunit [Influenza A virus (A/Georgia/1/67(H2N2))]. MERIKE...
15 Conclusions Not many trees had diverse likelihoods as to maximize the total likelihood Many of the sequences with large total likelihoods appeared in ducks and swine Many of the pairs that had a high score tend to have a polymerase unit in the pair
16 Thank You Questions?
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