A Review of of Recent De Developm lopment nts in in P Prot - PowerPoint PPT Presentation

A Review of of Recent De Developm lopment nts in in P Prot otein in Sequenc nce Ali lignm gnment Allyson Julian

Objectives ● Re Revi view of Li Literat atur ure (s (so no no indepe pend ndent nt evaluat uation/be /bench nchmarking) ng) ● Sum Summar arize us use of MSA fo for Pr Protein n Seque quenc nce Alignm gnment nt ● Appl pplicat ation n of f MSA SA al algo gorithms/m /methods ● Impl plementation n of f MS MSA al algo gorithms/m /methods ● Impr provements/enh nhan ancement nts inc nclud uded in n impl plement ntat ation 2 Allyson son Jul Julian

Why do we care? ● Pr Protein n alignm gnment nt info nforms struct uctur ural al analysis ● Evolut utiona nary co conservation ● Large ge pe pept ptide sequence nce read ads (m (millions – even n trillions in n size) ● Ho How do we ad address incr ncreas asing g size of f dat atas asets? ● Co Cons nstrai aint nts of cur current nt har ardwar are ● Limitations ns of cur urrent nt soft ftwar are ● Avai ailabi ability of publ publicl cly ac acce cessibl ble pe pept ptide/nucl /nucleotide dat atabas abases 3 Allyson son Jul Julian

Bioinformatics Background ● Se Seque quence nce alph phabe abet: 21 21 am amino no aci cids ● Alph phabe bet abo above us used to fo form string ng repr presentat ation n of f pe pept ptides ● Pai airwise al alignm gnment nts ● (Dis)simmilar arity sco cores ● Pr Profjl fjle HMM MM ● MAFF FFT ● T-co coff ffee 4 Allyson son Jul Julian

What will be summarized ● Input ● Met etho hodo dolog ogy ● MSA Algo SA Algorithms ms ● Enhan hancem emen ents ● Domain main-spe -specifj fjc knowled ledge ge ● Pr Protein/ in/geno nomic ic e external d al dat atab abase ses ● Output ● Re Resu sult lts ● Accurac acy (acc accordin ing g to au authors; s; will ill no not b be e evalu aluat atin ing g this m is myse self lf) ● Ru Runn nnin ing t g tim ime e (al (also so ac according ing t to aut authors) s) 5 Allyson son Jul Julian

Software to be explored ConS nSurf f 2016 2016 MAFFT PROS OSOM OMALS3D LS3D (2014) (2014) PSI/T /T-Coff ffee (2016) 2016) 6 Allyson son Jul Julian

Primary References [1] 1]H. H. Ashken enazy y et et al., , “ConSu Surf f 2016 2016: an impr improved ed methodo dolo logy to esti timate e and d vis isuali lize ev evolu lutio ionary conser ervatio tion in in macromolec lecules les,” ” Nucle leic Acids ids Res es, vol. l. 44, 44, no. W1, 1, pp. pp. W34 344– 4–W350, 350, Jul. l. 201 2016. 6. [2] 2]J. J. Pei ei and d N. Gris ishin in, , “PROMALS3D 3D: Mult ltipl iple Prote tein Seq equen ence Align lignment t Enhanced ed with th Evolu lutio tionary and d Th Three- ee-Dim imensio ional l Structu tural l Info formatio tion,” ” in in Multi ltiple ple Se Sequence e Align lignment t Met ethods ds, D. J. Russell, l, Ed. d. Hu Humana Pres ess, , 2014, 014, pp. pp. 263– 63–271. 71. [3] 3]E. W. Flo lode den, P . D. Tommaso, M. Chatz tzou, , C. Magis gis, , C. Notr treda edame, , and d J.-M. Chang, g, “PSI/ SI/TM-Coff ffee: e: a web eb server er fo for fa fast t and d accurate te mult ltiple iple seq equen ence e align lignments ts of f regu egular and d transme membr brane e pr protein eins usin ing g homo molo logy gy exten extension on redu educed ed databa bases,” ” Nucleic leic Acid ids Res es, vol. l. 44, 44, no. W1, 1, pp. p. W339– 39–W343, 343, Jul. l. 2016. 016. 7 Allyson son Jul Julian