Some frequently-used Bioinformatics Tools

MGM workshop. 19 Oct 2010

Some frequently-used Some frequently-used Bioinformatics ToolsBioinformatics Tools

Konstantinos Mavrommatis

Prokaryotic Superprogram


OutlineOutline

Pairwise Alignment Global/Local, Scoring BLAST, BLAT, SIM, LALIGN, Dotlet, Ublast

Multiple Sequence Alignment ClustalW, Kalign, MAFFT, Muscle, T-Coffee, MSA,

DIALIGN, Match-Box, Multalin, MUSCA

Phylogenetic analysis and tree construction BIONJ, DendroUPGMA, PHYLIP, PhyML, Phylogeny.fr,

POWER, BlastO, TraceSuite II

HMM Protein family profiles

http://expasy.org/tools/


AlignmentAlignment

Insert spaces in arbitrary locations -> same length and no two spaces in the same position.

Find arrangement of two sequences to identify regions of similarity


Alignment methods: Dot Alignment methods: Dot plotsplots


Global vs Local Global vs Local alignmentalignment

Global alignment: An alignment that assumes that the two sequences are basically similar over the entire length of one another

Local alignment: An alignment that searches for segments of the two sequences that match well

It may seem that one should always use local alignments! However each has its application


Substitution matricesSubstitution matrices

http://www.russelllab.org/aas/


Scoring an alignmentScoring an alignment


Global alignmentGlobal alignment

S1=HGSAQVKGHGS2=KTEAEMKASEDLKKHGT


KTEAEMKAESEDLKKHGT--HG--SA--Q-VKGHG-


Local AlignmentLocal Alignment


How BLAST worksHow BLAST works

MLVTTILAFALFKNSYAQQCGSQAGGALCSNRLCCSKFGYCGSTDPYCGTGCQSQCGGGG

VVWMLLVGGSYGVQCGTEAGGALCPRGLCCSQWGWCGSTIDYCGPGCQSQCGG

Common 3mer

GCQSQCGG extend

Query

Subject (database)

++ L SY QCG++AGGALC LCCS++G+CGST YCG GCQSQCGG

HSP

Score = 66.6 bits (161), Expect = 3e-12, Method: Compositional matrix adjust. Identities = 32/53 (60%), Positives = 39/53 (74%), Gaps = 0/53 (0%)

Query 6 ILAFALFKNSYAQQCGSQAGGALCSNRLCCSKFGYCGSTDPYCGTGCQSQCGG 58 ++ L SY QCG++AGGALC LCCS++G+CGST YCG GCQSQCGGSbjct 15 VVWMLLVGGSYGVQCGTEAGGALCPRGLCCSQWGWCGSTIDYCGPGCQSQCGG 67


Types of BlastTypes of Blast

Nucleic sequence:atcgatatatatagactgactgact

Protein sequence:MTAVYHILRALRARARVARARVH

6 frame translation

Nucleic acids sequence database

Nucleic acids sequence database

Protein seqeunces database

Protein seqeunces database

blastnblastn

blastpblastp

6 frame translationtblastxtblastx

blastxblastx

tblastntblastn

DatabaseQuery



Exact multiple alignment by Exact multiple alignment by dynamic programmingdynamic programming

Compexity= O(nS2SS2)N: length of sequencesS: number of sequences

Only feasible for 4-5 sequences max.



Neighbor JoiningNeighbor Joining


Unrooted NJ treeUnrooted NJ tree


Comparison of Multiple Comparison of Multiple sequence alignment sequence alignment

programsprograms


Primary sequence Primary sequence changes:changes:


ProfilesProfiles

CGGSV

0.8 * 0.4 * 0.8 * 0.6 * 0.2 = .031

ln(0.8)+ln(0.4)+ln(0.8)+ln(0.6)+ln(0.2) = -3.48


Hidden Markov ModelsHidden Markov Models

Assumptions: Observations are ordered Random process can be represented by a stochastic finite

state machine with emitting states

Probabilistic parameters of a Hidden Markov Model

x – states, y – possible observations

a – state transition probabilities, b –output/emision probabilities


HMM estimation, usage & HMM estimation, usage & applicationsapplications

Training/Estimation

Feed an architecture (given in advance) a set of observation sequences

The training process will iteratively alter its parameters to fit the training set

The trained model will assign the training sequences high probabilities

Usage

Evaluate the probability of an observation sequence given the model (Forward)

Find the most likely path through the model for a given observation sequence (Viterbi)

Applications

Gene finding

Protein family modeling

…


Profile HMMsProfile HMMs

Families of functional biological sequences Primary sequences have diverged due to evolution,

while maintaining structure/function. Questions:

Does a biological sequence belong to a certain protein family? For example is a given protein (sequence) a globin?

Given a set of sequences, find more sequences of the same family



Trade offsTrade offs

Advandages Disadvandages•Statistics•Modularity•Transparency•Prior knowledge

•State independence•Over – fitting•Local maximums•Speed


Questions?

Documents

Some frequently-used Bioinformatics Tools