Overview An introduction to multiple alignments · PDF fileAn introduction to multiple alignments ... wheat --DPNKPKRAPSAFFVFMGEFREEFKQKNPKNKSVAAVGKAAGERWKSLSE trybr KKDSNAPKRAMTSFMFFSSDFRS----KHSDLS-IVEMSKAAGAAWKELGP

Swiss Institute of Bioinf ormatics

Institut Suisse de Bioinf ormatique

CN+LF-2006.01

An introduction

to multiple alignmentsoriginal version by Cédric Notredame, updated by Laurent Falquet



CN+LF-2006.01

Overview

! Multiple alignments

! How-to, Goal, problems, use

! Patterns

! PROSITE database, syntax, use

! PSI-BLAST

! BLAST, matrices, use

! [ Profiles/HMMs ] …



CN+LF-2006.01

Overview

! What are multiple alignments?

! How can I use my alignments?

! How does the computer align the sequences?

! The progressive alignment algorithm

! What are the difficulties?

! Pre-requisite?

! How can we compare sequences?

! How can we align sequences?



CN+LF-2006.01

Sometimes two sequences are not enough

The man with TWO watches

NEVER knows the exact time



CN+LF-2006.01

What is a multiple sequence alignment?

! What can it do for me?

! How can I produce one of these?

! How can I use it?

chite ---ADKPKRPLSAYMLWLNSARESIKRENPDFK-VTEVAKKGGELWRGLKD

wheat --DPNKPKRAPSAFFVFMGEFREEFKQKNPKNKSVAAVGKAAGERWKSLSE

trybr KKDSNAPKRAMTSFMFFSSDFRS----KHSDLS-IVEMSKAAGAAWKELGP

mouse -----KPKRPRSAYNIYVSESFQ----EAKDDS-AQGKLKLVNEAWKNLSP

***. ::: .: .. . : . . * . *: *

chite AATAKQNYIRALQEYERNGG-

wheat ANKLKGEYNKAIAAYNKGESA

trybr AEKDKERYKREM---------

mouse AKDDRIRYDNEMKSWEEQMAE

* : .* . :



CN+LF-2006.01

What is a multiple sequence alignment?

! Structural/biochemical criteria! Residues playing a similar role end up in the same column.

! Evolution criteria! Residues having the same ancestor end up in the same column.





***. ::: .: .. . : . . * . *: *





* : .* . :



CN+LF-2006.01



CN+LF-2006.01

How can I use a multiple alignment?




unknown -----KPKRPRSAYNIYVSESFQ----EAKDDS-AQGKLKLVNEAWKNLSP

***. ::: .: .. . : . . * . *: *




unknown AKDDRIRYDNEMKSWEEQMAE

* : .* . :

Extrapolation

SwissProt

Unkown Sequence

Homology?

Less Than 30 % idBUT

Conserved where it MATTERS



CN+LF-2006.01






***. ::: .: .. . : . . * . *: *





* : .* . :

Extrapolation

Prosite Patterns

P-K-R-[PA]-x(1)-[ST]…



CN+LF-2006.01


Extrapolation

Prosite Patterns




mouse -----KPKRPRSAYNIYVSESFQ----EAKDDS-IQGKLKLVNEAWKNLSP

***. ::: .: .. . : . . * . *: *





* : .* . :

L?K>R

Prosite Profiles -More Sensitive

-More Specific

AFDEFGHQIVLW



CN+LF-2006.01

PROSITE profile (see also HMMs)

A Substitution Cost For Every Amino

Acid, At Every Position



CN+LF-2006.01


Phylogeny





***. ::: .: .. . : . . * . *: *





* : .* . :

chite

wheat

trybr

mouse

-Evolution

-Paralogy/Orthology



CN+LF-2006.01


Phylogeny





***. ::: .: .. . : . . * . *: *





* : .* . :

Struc. Prediction

Column Constraint"

Evolution Constraint"

Structure Constraint



CN+LF-2006.01


Phylogeny





***. ::: .: .. . : . . * . *: *





* : .* . :

Struc. Prediction

PsiPred or PhD

For secondary

Structure Prediction:

75% Accurate.

Threading: is improving

but is not yet as good.



CN+LF-2006.01


Phylogeny

Struc. Prediction





***. ::: .: .. . : . . * . *: *





* : .* . :

Caution!

Automatic Multiple

Sequence Alignment methods

are not always perfect…



CN+LF-2006.01



CN+LF-2006.01

The problem

! why is it difficult to compute a multiple sequencealignment?





***. ::: .: .. . : . . * . *: *

Computation

What is the good alignment?

Biology

What is a good alignment?



CN+LF-2006.01

The problem

! why is it difficult to compute a multiple sequencealignment?

CIRCULAR PROBLEM....

GoodSequences

GoodAlignment



CN+LF-2006.01

The problem

! Same as pairwise alignment problem

! We do NOT know how sequences evolve.

! We do NOT understand the relation betweenstructures and sequences.

! We would NOT recognize the “correct” alignment ifwe had it IN FRONT of our eyes…



CN+LF-2006.01

The Charlie Chaplin paradox



CN+LF-2006.01

What do I need to know to make a good multiple alignment?

! How do sequences evolve?

! How does the computer align the sequences?

! How can I choose my sequences?

! What is the best program?

! How can I use my alignment?



CN+LF-2006.01

An alignment is a story

ADKPKRPLSAYMLWLN

ADKPKRPLSAYMLWLN ADKPKRPLSAYMLWLN

ADKPRRPLS-YMLWLNADKPKRPKPRLSAYMLWLN

Mutations

+

Selection

ADKPRRP---LS-YMLWLNADKPKRPKPRLSAYMLWLN

Insertion

Deletion

Mutation



CN+LF-2006.01

Homology

! Same sequences -> same origin? -> same function? -> same 3D fold?

Length

%Sequence Identity

30%

100

Same 3D Fold

Twilight Zone



CN+LF-2006.01

Residues and mutations

! All residues are equal, but some more than others…

PG

SC

LI

T

V A

W

YF QH

K

R

ED N

Aliphatic

Aromatic

Hydrophobic

Polar

SmallM

Accurate matrices are data driven rather than knowledge driven

G

C



CN+LF-2006.01

Substitution matrices

Different Flavors:

• Pam: 250, 350• Blosum: 45, 62• …



CN+LF-2006.01

What is the best substitution matrix?

! Mutation rates depend on families

! Choosing the right matrix may be tricky

! Gonnet250 > BLOSUM62 > PAM250

! Depends on the family, the program used and its tuning

Family S NHistone3 6.4 0

Insulin 4.0 0.1

Interleukin I 4.6 1.4!"Globin 5.1 0.6

Apolipoprot. AI 4.5 1.6

Interferon G 8.6 2.8

Rates in Substitutions/site/Billion Years as measured on Mouse Vs Human (0.08 Billion years)



CN+LF-2006.01

Insertions and deletions?

Indel Cost

L

Cost

L

Cost

L

Affine Gap Penalty

Cost=GOP+GEP*L



CN+LF-2006.01

How to align many sequences?

! Exact algorithms are computing time consuming

! Needlemann & Wunsch

! Smith & Waterman

2 Globins =>1 sec



CN+LF-2006.01

3 Globins =>2 mn




! Smith & Waterman



CN+LF-2006.01

4 Globins =>5 hours




! Smith & Waterman

! -> heuristic wished



CN+LF-2006.01

5 Globins =>3 weeks




! Smith & Waterman

! -> heuristic really wished!



CN+LF-2006.01

6 Globins =>9 years




! Smith & Waterman

! -> heuristic required!



CN+LF-2006.01




! Smith & Waterman

! -> heuristic definitely required!

7 Globins =>1000 years



CN+LF-2006.01

Existing methods

1-Carillo and Lipman:

-MSA, DCA.

-Few Small Closely RelatedSequence.

2-Segment Based:

-DIALIGN, MACAW.

-May Align Too Few Residues

-Do Well When They Can Run.

3-Iterative:-HMMs, HMMER, SAM.

-Slow, Sometimes Inacurate

-Good Profile Generators

4-Progressive:

-ClustalW, Pileup, Multalign…

- Fast and Sensitive

5-Mixtures:

-T-Coffee, MAFFT, MUSCLE,ProbCons, Psi-Praline,

- Very sensitive



CN+LF-2006.01

Progressive alignment

Feng and Dolittle, 1980; Taylor 1981

Dynamic Programming Using A Substitution Matrix



CN+LF-2006.01


Feng and Dolittle, 1980; Taylor 1981

-Depends on the ORDER of the sequences (Tree).

-Depends on the CHOICE of the sequences.

-Depends on the PARAMETERS:

•Substitution Matrix.

•Penalties (Gop, Gep).

•Sequence Weight.

•Tree making Algorithm.



CN+LF-2006.01


! Works well when phylogeny is dense

! No outlayer sequence

! Example: river crossing



CN+LF-2006.01

Selecting sequences from a BLAST output



CN+LF-2006.01

A common mistake

! Sequences too closely related

! Identical sequences brings no information

! Multiple sequence alignments thrive on diversity

PRVA_MACFU SMTDLLNAEDIKKAVGAFSAIDSFDHKKFFQMVGLKKKSADDVKKVFHILDKDKSGFIEE

PRVA_HUMAN SMTDLLNAEDIKKAVGAFSATDSFDHKKFFQMVGLKKKSADDVKKVFHMLDKDKSGFIEE

PRVA_GERSP SMTDLLSAEDIKKAIGAFAAADSFDHKKFFQMVGLKKKTPDDVKKVFHILDKDKSGFIEE

PRVA_MOUSE SMTDVLSAEDIKKAIGAFAAADSFDHKKFFQMVGLKKKNPDEVKKVFHILDKDKSGFIEE

PRVA_RAT SMTDLLSAEDIKKAIGAFTAADSFDHKKFFQMVGLKKKSADDVKKVFHILDKDKSGFIEE

PRVA_RABIT AMTELLNAEDIKKAIGAFAAAESFDHKKFFQMVGLKKKSTEDVKKVFHILDKDKSGFIEE

:**::*.*******:***:* :****************..::******:***********

PRVA_MACFU DELGFILKGFSPDARDLSAKETKTLMAAGDKDGDGKIGVDEFSTLVAES

PRVA_HUMAN DELGFILKGFSPDARDLSAKETKMLMAAGDKDGDGKIGVDEFSTLVAES

PRVA_GERSP DELGFILKGFSSDARDLSAKETKTLLAAGDKDGDGKIGVEEFSTLVSES

PRVA_MOUSE DELGSILKGFSSDARDLSAKETKTLLAAGDKDGDGKIGVEEFSTLVAES

PRVA_RAT DELGSILKGFSSDARDLSAKETKTLMAAGDKDGDGKIGVEEFSTLVAES

PRVA_RABIT EELGFILKGFSPDARDLSVKETKTLMAAGDKDGDGKIGADEFSTLVSES

:*** ******.******.**** *:************.:******:**



CN+LF-2006.01



CN+LF-2006.01

Respect information!

-This alignment is notinformative about therelation between TPCCMOUSE and the rest ofthe sequences.

-A better spread of thesequences is needed

PRVA_MACFU ------------------------------------------SMTDLLN----AEDIKKA

PRVA_HUMAN ------------------------------------------SMTDLLN----AEDIKKA

PRVA_GERSP ------------------------------------------SMTDLLS----AEDIKKA

PRVA_MOUSE ------------------------------------------SMTDVLS----AEDIKKAPRVA_RAT ------------------------------------------SMTDLLS----AEDIKKA

PRVA_RABIT ------------------------------------------AMTELLN----AEDIKKA

TPCC_MOUSE MDDIYKAAVEQLTEEQKNEFKAAFDIFVLGAEDGCISTKELGKVMRMLGQNPTPEELQEM

: :*. .*::::

PRVA_MACFU VGAFSAIDS--FDHKKFFQMVG------LKKKSADDVKKVFHILDKDKSGFIEEDELGFI

PRVA_HUMAN VGAFSATDS--FDHKKFFQMVG------LKKKSADDVKKVFHMLDKDKSGFIEEDELGFI

PRVA_GERSP IGAFAAADS--FDHKKFFQMVG------LKKKTPDDVKKVFHILDKDKSGFIEEDELGFIPRVA_MOUSE IGAFAAADS--FDHKKFFQMVG------LKKKNPDEVKKVFHILDKDKSGFIEEDELGSI

PRVA_RAT IGAFTAADS--FDHKKFFQMVG------LKKKSADDVKKVFHILDKDKSGFIEEDELGSI

PRVA_RABIT IGAFAAAES--FDHKKFFQMVG------LKKKSTEDVKKVFHILDKDKSGFIEEEELGFI

TPCC_MOUSE IDEVDEDGSGTVDFDEFLVMMVRCMKDDSKGKSEEELSDLFRMFDKNADGYIDLDELKMM :. . * .*..:*: *: * *. :::..:*:::**: .*:*: :** :

PRVA_MACFU LKGFSPDARDLSAKETKTLMAAGDKDGDGKIGVDEFSTLVAES-

PRVA_HUMAN LKGFSPDARDLSAKETKMLMAAGDKDGDGKIGVDEFSTLVAES-PRVA_GERSP LKGFSSDARDLSAKETKTLLAAGDKDGDGKIGVEEFSTLVSES-

PRVA_MOUSE LKGFSSDARDLSAKETKTLLAAGDKDGDGKIGVEEFSTLVAES-

PRVA_RAT LKGFSSDARDLSAKETKTLMAAGDKDGDGKIGVEEFSTLVAES-

PRVA_RABIT LKGFSPDARDLSVKETKTLMAAGDKDGDGKIGADEFSTLVSES-TPCC_MOUSE LQ---ATGETITEDDIEELMKDGDKNNDGRIDYDEFLEFMKGVE

*: . .. :: .: : *: ***:.**:*. :** ::



CN+LF-2006.01

Selecting diverse sequences

-A REASONABLE model now exists.

-Going further:remote homologues.

PRVB_CYPCA -AFAGVLNDADIAAALEACKAADSFNHKAFFAKVGLTSKSADDVKKAFAIIDQDKSGFIEPRVB_BOACO -AFAGILSDADIAAGLQSCQAADSFSCKTFFAKSGLHSKSKDQLTKVFGVIDRDKSGYIEPRV1_SALSA MACAHLCKEADIKTALEACKAADTFSFKTFFHTIGFASKSADDVKKAFKVIDQDASGFIEPRVB_LATCH -AVAKLLAAADVTAALEGCKADDSFNHKVFFQKTGLAKKSNEELEAIFKILDQDKSGFIEPRVB_RANES -SITDIVSEKDIDAALESVKAAGSFNYKIFFQKVGLAGKSAADAKKVFEILDRDKSGFIEPRVA_MACFU -SMTDLLNAEDIKKAVGAFSAIDSFDHKKFFQMVGLKKKSADDVKKVFHILDKDKSGFIEPRVA_ESOLU --AKDLLKADDIKKALDAVKAEGSFNHKKFFALVGLKAMSANDVKKVFKAIDADASGFIE : *: .: . .* .:*. * ** *: * : * :* * **:**

PRVB_CYPCA EDELKLFLQNFKADARALTDGETKTFLKAGDSDGDGKIGVDEFTALVKA-PRVB_BOACO EDELKKFLQNFDGKARDLTDKETAEFLKEGDTDGDGKIGVEEFVVLVTKGPRV1_SALSA VEELKLFLQNFCPKARELTDAETKAFLKAGDADGDGMIGIDEFAVLVKQ-PRVB_LATCH DEELELFLQNFSAGARTLTKTETETFLKAGDSDGDGKIGVDEFQKLVKA-PRVB_RANES QDELGLFLQNFRASARVLSDAETSAFLKAGDSDGDGKIGVEEFQALVKA-PRVA_MACFU EDELGFILKGFSPDARDLSAKETKTLMAAGDKDGDGKIGVDEFSTLVAESPRVA_ESOLU EEELKFVLKSFAADGRDLTDAETKAFLKAADKDGDGKIGIDEFETLVHEA :** .*:.* .* *: ** :: .* **** **::** **



CN+LF-2006.01

Aligning remote homologuesPRVA_MACFU ------------------------------------------SMTDLLNA----EDIKKAPRVA_ESOLU -------------------------------------------AKDLLKA----DDIKKA

PRVB_CYPCA ------------------------------------------AFAGVLND----ADIAAA

PRVB_BOACO ------------------------------------------AFAGILSD----ADIAAG

PRV1_SALSA -----------------------------------------MACAHLCKE----ADIKTAPRVB_LATCH ------------------------------------------AVAKLLAA----ADVTAA

PRVB_RANES ------------------------------------------SITDIVSE----KDIDAA

TPCS_RABIT -TDQQAEARSYLSEEMIAEFKAAFDMFDADGG-GDISVKELGTVMRMLGQTPTKEELDAI

TPCS_PIG -TDQQAEARSYLSEEMIAEFKAAFDMFDADGG-GDISVKELGTVMRMLGQTPTKEELDAITPCC_MOUSE MDDIYKAAVEQLTEEQKNEFKAAFDIFVLGAEDGCISTKELGKVMRMLGQNPTPEELQEM

: ::

PRVA_MACFU VGAFSAIDS--FDHKKFFQMVG------LKKKSADDVKKVFHILDKDKSGFIEEDELGFIPRVA_ESOLU LDAVKAEGS--FNHKKFFALVG------LKAMSANDVKKVFKAIDADASGFIEEEELKFV

PRVB_CYPCA LEACKAADS--FNHKAFFAKVG------LTSKSADDVKKAFAIIDQDKSGFIEEDELKLF

PRVB_BOACO LQSCQAADS--FSCKTFFAKSG------LHSKSKDQLTKVFGVIDRDKSGYIEEDELKKF

PRV1_SALSA LEACKAADT--FSFKTFFHTIG------FASKSADDVKKAFKVIDQDASGFIEVEELKLFPRVB_LATCH LEGCKADDS--FNHKVFFQKTG------LAKKSNEELEAIFKILDQDKSGFIEDEELELF

PRVB_RANES LESVKAAGS--FNYKIFFQKVG------LAGKSAADAKKVFEILDRDKSGFIEQDELGLF

TPCS_RABIT IEEVDEDGSGTIDFEEFLVMMVRQMKEDAKGKSEEELAECFRIFDRNADGYIDAEELAEI

TPCS_PIG IEEVDEDGSGTIDFEEFLVMMVRQMKEDAKGKSEEELAECFRIFDRNMDGYIDAEELAEITPCC_MOUSE IDEVDEDGSGTVDFDEFLVMMVRCMKDDSKGKSEEELSDLFRMFDKNADGYIDLDELKMM

: . .: .. . *: * : * :* : .*:*: :** .

PRVA_MACFU LKGFSPDARDLSAKETKTLMAAGDKDGDGKIGVDEFSTLVAES-PRVA_ESOLU LKSFAADGRDLTDAETKAFLKAADKDGDGKIGIDEFETLVHEA-

PRVB_CYPCA LQNFKADARALTDGETKTFLKAGDSDGDGKIGVDEFTALVKA--

PRVB_BOACO LQNFDGKARDLTDKETAEFLKEGDTDGDGKIGVEEFVVLVTKG-

PRV1_SALSA LQNFCPKARELTDAETKAFLKAGDADGDGMIGIDEFAVLVKQ--

PRVB_LATCH LQNFSAGARTLTKTETETFLKAGDSDGDGKIGVDEFQKLVKA--PRVB_RANES LQNFRASARVLSDAETSAFLKAGDSDGDGKIGVEEFQALVKA--

TPCS_RABIT FR---ASGEHVTDEEIESLMKDGDKNNDGRIDFDEFLKMMEGVQ

TPCS_PIG FR---ASGEHVTDEEIESIMKDGDKNNDGRIDFDEFLKMMEGVQ

TPCC_MOUSE LQ---ATGETITEDDIEELMKDGDKNNDGRIDYDEFLEFMKGVE

:: .. :: : :: .* :.** *. :** ::



CN+LF-2006.01

Going further…

PRVA_MACFU VGAFSAIDS--FDHKKFFQMVG------LKKKSADDVKKVFHILDKDKSGFIEEDELGFI

PRVB_BOACO LQSCQAADS--FSCKTFFAKSG------LHSKSKDQLTKVFGVIDRDKSGYIEEDELKKF

PRV1_SALSA LEACKAADT--FSFKTFFHTIG------FASKSADDVKKAFKVIDQDASGFIEVEELKLF

TPCS_RABIT IEEVDEDGSGTIDFEEFLVMMVRQMKEDAKGKSEEELAECFRIFDRNADGYIDAEELAEI

TPCS_PIG IEEVDEDGSGTIDFEEFLVMMVRQMKEDAKGKSEEELAECFRIFDRNMDGYIDAEELAEI

TPCC_MOUSE IDEVDEDGSGTVDFDEFLVMMVRCMKDDSKGKSEEELSDLFRMFDKNADGYIDLDELKMM

TPC_PATYE SDEMDEEATGRLNCDAWIQLFER---KLKEDLDERELKEAFRVLDKEKKGVIKVDVLRWI

. : .. . :: . : * :* : .* *. : * .

PRVA_MACFU LKGFSPDARDLSAKETKTLMAAGDKDGDGKIGVDEFSTLVAES--

PRVB_BOACO LQNFDGKARDLTDKETAEFLKEGDTDGDGKIGVEEFVVLVTKG--

PRV1_SALSA LQNFCPKARELTDAETKAFLKAGDADGDGMIGIDEFAVLVKQ---

TPCS_RABIT FR---ASGEHVTDEEIESLMKDGDKNNDGRIDFDEFLKMMEGVQ-

TPCS_PIG FR---ASGEHVTDEEIESIMKDGDKNNDGRIDFDEFLKMMEGVQ-

TPCC_MOUSE LQ---ATGETITEDDIEELMKDGDKNNDGRIDYDEFLEFMKGVE-

TPC_PATYE LS---SLGDELTEEEIENMIAETDTDGSGTVDYEEFKCLMMSSDA

: . :: : :: * :..* :. :** ::



CN+LF-2006.01

What makes a good alignment…

! The more divergent the sequences, the better

! The fewer indels, the better

! Nice ungapped blocks separated with indels

! Different classes of residues within a block:

! Completely conserved (*)

! Size and hydropathy conserved (:)

! Size or hydropathy conserved (.)

! The ultimate evaluation is a matter of personaljudgment and knowledge



CN+LF-2006.01

Avoiding pitfalls



CN+LF-2006.01

Naming your sequences the right way

! Never use white spaces in your sequence names

! Never use special symbols. Stick to plain letters,numbers and the underscore sign (_) to replacespaces. Avoid ALL other signs, especially the mosttempting ones like @, #, |, *, >, <…

! Never use names longer than 15 characters

! Never give the same name to 2 different sequencesin your set. Some programs accept it, others likeClustalW don’t.



CN+LF-2006.01

Do not use too many sequences!



CN+LF-2006.01

Beware of Repeats

! There is a problem when two sequences do not contain the same number ofrepeats

! It is then better to manually extract the repeats and to align them separately.Individual repeats can be recognized using Dotlet or Dotter.



CN+LF-2006.01

Keep a biological perspective





***. ::: .: .. . : . . * . *: *





* : .* . :

chite AD--K----PKR-PLYMLWLNS-ARESIKRENPDFK-VT-EVAKKGGELWRGL-

wheat -DPNK----PKRAP-FFVFMGE-FREEFKQKNPKNKSVA-AVGKAAGERWKSLS

trybr -K--KDSNAPKR-AMT-MFFSSDFR-S-KH-S-DLS-IV-EMSKAAGAAWKELG

mouse ----K----PKR-PRYNIYVSESFQEA-K--D-D-S-AQGKL-KLVNEAWKNLS

* *** .:: ::... : * . . . : * . *: *

chite KSEWEAKAATAKQNY-I--RALQE-YERNG-G-

wheat KAPYVAKANKLKGEY-N--KAIAA-YNK-GESA

trybr RKVYEEMAEKDKERY----K--RE-M-------

mouse KQAYIQLAKDDRIRYDNEMKSWEEQMAE-----

: : * : .* :

DIFFERENTPARAMETERS



CN+LF-2006.01

Do not overtune!!!

DO NOT PLAY WITHPARAMETERS!

IF YOU KNOW THEALIGNMENT YOU

WANT:MAKE IT YOURSELF!





***. ::: .: .. . : . . * . *: *





* : .* . :

chite ---ADKPKRPL-SAYMLWLNSARESIKRENPDFK-VTEVAKKGGELWRGLKD

wheat --DPNKPKRAP-SAFFVFMGEFREEFKQKNPKNKSVAAVGKAAGERWKSLSE

trybr KKDSNAPKRAMTSFMFFSSDFRS-----KHSDLS-IVEMSKAAGAAWKELGP

mouse -----KPKRPR-SAYNIYVSESFQ----EAKDDS-AQGKLKLVNEAWKNLSP

***. * .: .. . : . . * . *: *





* : .* . :



CN+LF-2006.01

BaliBase classification and benchmark

DescriptionPROBLEM

EvenPhylogenicSpread.

One OutlayerSequence

Two Distantlyrelated Groups

Long InternalIndel

Long TerminalIndel



CN+LF-2006.01

Choosing the right method

Source:

BaliBase

Thompsonet al, NAR,

(1999)

Do et al,Genome

Res. (2005)

PROBLEM Program Strategy

ClustalW,T-coffee,

MUSCLE,ProbCons

ProbCons,MUSCLE,MAFFT

Dialign II,ProbCons,

T-Coffee

T-Coffee,MUSCLE,ProbCons

Dialign II,

ProbCons,

MAFFT



CN+LF-2006.01

Some interesting links



CN+LF-2006.01

More links

! MUSCLE

! http://www.drive5.com/muscle

! MAFFT

! http://timpani.genome.ad.jp/~mafft/server

! PROBCONS

! http://probcons.stanford.edu

! PSI-PRALINE

! http://ibivu.cs.vu.nl/programs/pralinewww

! 3D-COFFEE! http://www.igs.cnrs-mrs.fr/Tcoffee/tcoffee_cgi/index.cgi



CN+LF-2006.01

Conclusion

! The best alignment method:

! Your brain

! The right data

! The best evaluation method:

! Your eyes

! Experimental information(SwissProt)

! Choosing the sequences well isimportant

! Beware of repeated elements

! What can I conclude?

! Homology -> informationextrapolation

! How can I go further?

! Patterns

! Profiles

! HMMs

! …

Documents

Overview An introduction to multiple alignments · PDF fileAn introduction to multiple alignments ... wheat --DPNKPKRAPSAFFVFMGEFREEFKQKNPKNKSVAAVGKAAGERWKSLSE trybr KKDSNAPKRAMTSFMFFSSDFRS----KHSDLS-IVEMSKAAGAAWKELGP