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

A Review of

• f Recent De

Developm lopment nts in in P Prot

• tein

in Sequenc nce Ali lignm gnment

Allyson Julian

Allyson son Jul Julian 2

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

Allyson son Jul Julian 3

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

Allyson son Jul Julian 4

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

Allyson son Jul Julian 5

What will be summarized

• Input
• Met

etho hodo dolog

• gy
• 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)

Allyson son Jul Julian 6

Software to be explored

ConS nSurf f 2016 2016 MAFFT PROS OSOM OMALS3D LS3D (2014) (2014) PSI/T /T-Coff ffee (2016) 2016)

Allyson son Jul Julian 7

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.