4. Profile HMMs - eclass.uoa.gr · Profile HMMs for sequence families 1. So far we have concentrated on the intrinsic properties of single sequences , such as CpGislands . 2. However

Profile HMMs for sequence families

1. So far we have concentrated on the intrinsic properties of single sequences,

such as CpG islands.

2. However functional biological sequences typically come in families, so what

we are after is identifying the relationship of an individual sequences to a

sequence family.

3. A multiple sequence alignment can show how the sequences in a family

relate to each other.

4. Some positions in a multiple sequence alignment are more conserved than

others (e.g. helices as opposed to loop regions).

5. Therefore it would be desirable, when identifying new sequence members to

concentrate more on conserved features.

6. For this task we will discuss a special type of HMM, well suited to modelling

multiple alignments; we will call these profile HMMs.

7. Profile HMMs are the most popular application of HMMs in molecular biology.






sequence family.















sequence family.















sequence family.















sequence family.















sequence family.















sequence family.










Position specific score matrix

A common feature of protein multiple sequence alignments is that gaps tend to line up

with each other, leaving solid blocks with no insertions or deletions.

A probabilistic model for a conserved region (block) would be to specify independent

probabilities ei(α) of observing amino acid α in position i. The probability of a new

sequence x, is:

where L is the length of the block. To test for family membership we evaluate, as usual

log-odds ratio:

The values log(ei(a)/qa) behave like elements in a score matrix s(a, b) where the

second index is position i, rather than amino acid b.

Such an approach is known as a position specific score matrix (PSSM).






sequence x, is:


log-odds ratio:




1

( | ) ( )L

i i

i

P x M e x=

=∏






sequence x, is:


log-odds ratio:




1

( | ) ( )L

i i

i

P x M e x=

=∏

1

( )log

i

Li i

i x

e xS

q=

=∑






sequence x, is:


log-odds ratio:




1

( | ) ( )L

i i

i

P x M e x=

=∏

1

( )log

i

Li i

i x

e xS

q=

=∑

Profile HMMs: αs and es

Profile HMMs: transition structure

•Match

•Insertion

•Deletion

Profile HMMs: Viterbi

Let VjM(i) be the log-odds score of the best path matching

subsequence x1…i to the submodel up to state j, ending with xi being emitted by state Mj (match).

Similarly VjI(i), Vj

D(i) are the scores for state Ij (insertion) and Dj(deletion) respectively.

Then we can write:

Profile HMMs: Viterbi

Let VjM(i) be the log-odds score of the best path matching

subsequence x1…i to the submodel up to state j, ending with xi being emitted by state Mj (match).

Similarly VjI(i), Vj

D(i) are the scores for state Ij (insertion) and Dj(deletion) respectively.

Then we can write:

Profile HMMs: model construction

v

Begin

Begin

((

(

(

(

(

(

((( (

((

End

End

hmmalign - align sequences to a profile HMM

hmmbuild - construct profile HMM(s) from multiple sequence alignment(s)

hmmconvert - convert profile file to a HMMER format

hmmemit - sample sequences from a profile HMM

hmmfetch - retrieve profile HMM(s) from a file

hmmpress - prepare an HMM database for hmmscan

hmmscan - search sequence(s) against a profile database

hmmsearch - search profile(s) against a sequence database

hmmsim - collect score distributions on random sequences

hmmstat - display summary statistics for a profile file

jackhmmer - iteratively search sequence(s) against a protein database

phmmer - search protein sequence(s) against a protein sequence database

SOURCE: http://hmmer.janelia.org/

HMMER














HMMER














HMMER














HMMER














HMMER














HMMER














HMMER














HMMER














HMMER














HMMER














HMMER














HMMER

the number of

match states in

the model.

Symbol alphabet

type

the number of

sequences that the

HMM was trained on

the number of

match states in

the model.

Symbol alphabet

type

the number of

sequences that the

HMM was trained on

the effective total number

of sequences determined

by hmmbuild during

sequence weighting, for

combining observed

counts with Dirichlet prior

information in

parameterizing the model

the number of

match states in

the model.

Symbol alphabet

type

the number of

sequences that the

HMM was trained on



by hmmbuild during


combining observed


information in


This number is calculated

from the training sequence

data, and used in conjunction

with the alignment map

information to verify that a

given alignment is indeed the

alignment that the map is for

the number of

match states in

the model.

Symbol alphabet

type

Reference annotation flag;.Reference

column annotation is picked up from a

Stockholm alignment file’s #=GC RF line.

the number of

sequences that the

HMM was trained on



by hmmbuild during


combining observed


information in









the number of

match states in

the model.

Symbol alphabet

type




Consensus structure annotation flag; is picked

up from a Stockholm file’s #=GC SS_cons line

the number of

sequences that the

HMM was trained on



by hmmbuild during


combining observed


information in









the number of

match states in

the model.

Symbol alphabet

type




Consensus structure annotation flag; is picked

up from a Stockholm file’s #=GC SS_cons line

Map annotation flag. The HMM/alignment map

annotates each match state with the index of the

alignment column from which it came. It can be

used for quickly mapping any subsequent HMM

alignment back to the original multiple alignment,

via the model

the number of

sequences that the

HMM was trained on



by hmmbuild during


combining observed


information in









Statistical parameters

needed for E-value

calculations.

Flags the start of the

main model section


needed for E-value

calculations.

Flags the start of the

main model section

these are the model’s

overall average match

state emission

probabilities, which are

used as a background

residue composition in the

“filter null” model.


needed for E-value

calculations.

contains information for the core model’s BEGIN node. This is

stored as model node 0, and match state 0 is treated as the BEGIN

state.

The begin state is mute, so there are no match emission

probabilities. The first line is the insert 0 emissions. The second line

contains the transitions from the begin state and insert state 0.

These seven numbers are:

B → M1, B → I0, B → D1; I0 → M1, I0 → I0;

then a 0.0 and a ’*’, because by convention, nonexistent

transitions from the nonexistent delete state 0 are set to log 1 = 0

and log 0 = -∞ = ‘*’.

Line 1: Match emission line

Line 2: Insert emission line

Line 3: State transition line




the MAP annotation

the RF annotation

the CS annotation

… for this node




score: The bit score for this

domain.


domain.

The biased composition

(null2) score correction that

was applied to the domain bit

score.


domain.




score.

The “conditional E-value”, a

permissive measure of how reliable

this particular domain

may be. The conditional E-value is

calculated on a smaller search

space than the independent

Evalue. The conditional E-value

uses the number of targets that

pass the reporting thresholds.


domain.




score.










The “independent E-value”, the E-

value that the sequence/profile

comparison would have

received if this were the only

domain envelope found in it,

excluding any others. This is a

stringent measure of how reliable

this particular domain may be. The

independent E-value uses the total

number of targets in the target

database.


domain.




score.




















database.

The mean posterior

probability of aligned

residues in the alignment;

a measure of how reliable

the overall alignment is


domain.




score.




















database.

The start/end of the domain envelope on the

sequence, numbered 1..L for a sequence

of L residues. The envelope defines a

subsequence for which their is substantial

probability mass supporting a homologous

domain

The mean posterior






domain.




score.




















database.

The start/end of the alignment

of this domain with respect to

the sequence






domain

The mean posterior






domain.




score.




















database.



the profile



the sequence






domain

The mean posterior





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4. Profile HMMs - eclass.uoa.gr · Profile HMMs for sequence families 1. So far we have concentrated on the intrinsic properties of single sequences , such as CpGislands . 2. However