eric nawrocki sean eddy’s labtandy/nawrocki-symposium.pdftree building program. de novo multiple...

Multiple alignment using sequence family profiles

Eric Nawrocki

Sean Eddy’s Lab

Howard Hughes Medical InstituteJanelia Farm Research Campus

Small subunit ribosomal RNA and the tree of life

• 1977 - Carl Woese decided to classify allliving things phylogenetically

• needed “a molecule of appropriatelybroad distribution” for comparativeanalysis

• SSU rRNA was chosen

– universally distributed

– highly conserved

– large enough to provide sufficientdata (1500-1800 nt)

– readily isolated

Pace, Science:276; 1997

**

*

Universal conservation of SSU rRNA

Escherichia coli Methanococcus vannielii Zea mays

Secondary structure diagrams from:URL:http://www.rna.ccbb.utexas.edu/

Environmental surveys target SSU

• mid 1980s - Norman Pace develops methodology fordetermination of SSU sequences without cultivation

• many different environments have been surveyed

• known biodiversity has been greatly expanded:

– recognized bacterial phyla:11 in 1987, 36 in 1998, 52 in 2003, 67 in 2006...

• SSU databases contain millions of sequences:

name # seqs # citationsSilva 3.2M 1125RDP 2.6M 1170Greengenes 1.0M 1012

Silva: Pruesse et al., 2007 NAR 35.21:7188-96RDP: Cole et al., 2009 NAR 37:D141-45Greengenes: DeSantis et al., 2006 AEM 72:5069-72

PCR

rRNA/rDNAsequences

genomicsequence

genomiclibrary

sequencing

cloning

extraction

sampleenvironmental

rRNA/rDNA

rRNA/rDNAclones

community

shotgunsequencing

treesphylogenetic

adapted from: Hugenholtz,

Genome Biology:2002 3(2)

bulk RNA/DNA

cloning

analysiscomparative

The comparative analysis step:

Alignment and Phylogenetic Inference

Goals of the alignment program:- accurate: because alignment errors confound phylogenetic inference- scalable to handle up to millions of seqs and fast:

Information that can help:- many known sequences- manually curated SSU alignments- known secondary structure of SSU

SSU tree

SSU alignment

SSU sequences

alignmentprogram

tree buildingprogram


De novo multiple sequence alignment methods assume very little

progressive alignment

aligned sequences

alignment polishing

hierarchical clustering(minimum spanning tree,UPGMA)

guidetree

Drawbacks for SSU alignment:1. Won’t scale to millions of seqs (O(N^2))2. Ignores previous knowledge of SSU

N^2 comparisons(pairwise alignment,K-mer counting)

N^2 distancematrix

input sequences:

Assumption:These sequences are homologous.

A trusted (probably manually curated) reference alignment can help

3. Add to new alignment

trusted alignment:

"nearest neighbor" alignment:

2. pairwise alignmentto nearest neighbor

new sequences:

1. Find nearest neighbor

?

?

?

?} N seqs

Mseqs{

Advantages over de novo:1. More scalable (O(MN))2. Uses existing, trusted SSU alignment

Drawbacks:1. Still slow if M is large (~5000 for Greengenes)2. Pairwise alignment ignores varying conservation across alignment

Profile-based alignment is O(N)

profile

alignment

new sequences:

trusted alignment (”seed”):

Advantages over de novo and nearest-neighbor:1. Scalable (O(N))2. Uses existing, trusted SSU alignment3. Uses position-specific scores

Drawbacks:1. Only consensus positions are aligned, other nucleotides are inserted2. Ignorant of phylogeny

Profiles have position-specific scores

(substitutions, gap open, gap extend)

1 8764321 876432

yeast GUCaUUCGGC...ACfly GCC.UU-GGA...GCcow GCA.UUCGUC...-Cmouse GCA.UU-GAU...GChuman GCGaUUCGCU...GCchicken GUA.UUCGUA...ACsnake GUGaUUCGCG...ACcroc GUU.UU-GAG...AC

GUCACGU U55UCG

11C

1010GAACGU

99

ACGU

worm G-G.UUCGCGccaACstarfish G-U.UUCGAU...-C

sequenceprofile

Profiles HMMs are probabilistic profiles built from alignments

M

I

D

M

I

D

UC

2

One HMM node peralignment column

P(C) = 0.5P(U) = 0.5

transitions

3 states per node:(M) Match: emits residues (I) Insert: inserts extra residues(D) Delete: deletes residues

HMMs generate homologoussequences.

Node for column 2:

transitions

Given a sequence, the most likelypath that could have generatedthat sequence can be computed.This path implies an alignment.

G UCACGU U U C G CG

AACGU

ACGUM

I

D

M

I

D

M

I

D

M

I

D

M

I

D

M

I

D

M

I

D

M

I

D

M

I

D

MB

II

D

EM

I

D

M

I

D

M

I

D

M

I

D

M

I

D

M

I

D

M

I

D

M

I

D

M

I

D

M

I

D

MB

II

D

EM

I

D

1 5 11109876432 118

1 8764321 876432


GUCACGU U55UCG

11C

1010GAACGU

99

ACGU


Sequences are aligned to profiles HMMs using dynamic programming

algorithms very similar to Smith-Waterman

M

I

D

M

I

D

UC

2

One HMM node peralignment column

P(C) = 0.5P(U) = 0.5

transitions

3 states per node:(M) Match: emits residues (I) Insert: inserts extra residues(D) Delete: deletes residues

HMMs generate homologoussequences.

Node for column 2:

transitions

Given a sequence, the most likelypath that could have generatedthat sequence can be computed.This path implies an alignment.

G UCACGU U U C G CG

AACGU

ACGUM

I

D

M

I

D

M

I

D

M

I

D

M

I

D

M

I

D

M

I

D

M

I

D

M

I

D

MB

II

D

EM

I

D

M

I

D

M

I

D

M

I

D

M

I

D

M

I

D

M

I

D

M

I

D

M

I

D

M

I

D

MB

II

D

EM

I

D

1 5 11109876432 118

MMMMMMMMMB EM

urchin

MMMMMMMMMB EM

G U U U U C CAA A

urchin GUU.UUC-AA...AC

DD

1 8764321 876432


GUCACGU U55UCG

11C

1010GAACGU

99

ACGU


Profile alignment can differ from pairwise alignment

Pairwise alignmentto nearest neighbor

starfish GUUUCGAUCurchin GUUUUCAAAC

starfish G-UUUCGAUCurchin GUUUUCAAAC * **** * *

1 8764321 876432


GUCACGU U55UCG

11C

1010GAACGU

99

ACGU

worm G-G.UUCGCGccaACstarfish G-U.UUCGAU...-Curchin GUU.UUC-AA...AC

yeast GUCaUUCGGC...ACfly GCC.UU-GGA...GCcow GCA.UUCGUC...-Cmouse GCA.UU-GAU...GChuman GCGaUUCGCU...GCchicken GUA.UUCGUA...ACsnake GUGaUUCGCG...ACcroc GUU.UU-GAG...ACworm G-G.UUCGCGccaACstarfish G-U.UUCGAU...-Curchin GUU.UUCAAA...-C

1 8764321 876432GUCACGU U

55UCG

11C

1010GAACGU

99

ACGU

5ʼ

3ʼ

100

200

300

400

500

600

700

800

900

1000

1100

1200

1300

1400

1500

Sequence conservation per position blue: highly conserved ...... red: highly variable

created by the SSU-ALIGN packagestructure diagram derived from CRW database (http://www.rna.ccbb.utexas.edu/)

5ʼ

3ʼ

100

200

300

400

500

600

700

800

900

1000

1100

1200

1300

1400

1500

Frequency of insertions after each positiongrey: zero to very few inserts ...... teal: 1-2% inserts

5ʼ

3ʼ

100

200

300

400

500

600

700

800

900

1000

1100

1200

1300

1400

1500

Sequence conservation per position blue: highly conserved ...... red: highly variable


Secondary structure (mutual) information per positionblue: low information ...... red: high information

5ʼ

3ʼ

100

200

300

400

500

600

700

800

900

1000

1100

1200

1300

1400

1500

Covariance models (CMs) are built

from structure-annotated alignments

32

4 14

5 1312

6 117 10

8 9

15

16 27

17 2618

19 25

21 2322

guide tree:

AA

G C

A UA

C GU G

U C

U

G C

G CC

G C

A AC

input multiple alignment:

AUA

:AAG

:GCG

<AAU

<CCC

<UUU

:UUU

:CCC

:GG-

:GGG

>AAC

:UUA

>CGC

>U-G

:GCG

<GAG

<CCC

:GCA

<AAC

:CAC

:AAA

:CGU

>CUU

>CGC

>humanmouse

orc

[structure]

g...

c...

.a..

.a..

1 5 10 15 20 25 28

example structure(human):

states for 3 guide tree nodes:A C

B

16

17

18

ROOT

MATL2

MATL3

BIF

4 14

5 13

12

6 11

7

8

9

10

BEGL

MATP

MATP

MATR

MATP

MATL

MATL

MATL

MATL

END

BEGR

MATL15

MATP16 27

MATP17 26

MATL18

MATP19 25

MATL21

MATL22

MATL23

END

MATP

MATP

MATL

MP ML MR D

IL IR

MP ML MR D

IL IR

ML D

IL

62 63

50 51 52 53

54 55

56 57 58 59

60 61

64

0

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

Benchmark of SSU alignment

• How accurate are profile-based alignments?

• ’Gold standard’ testing dataset

– structural alignment of 152 bacterial SSU sequences from Robin Gutell’s database

– this is the CRW bacterial seed alignment filtered to 92% identity

– determined by ’manual’ comparative analysis

51 test sequences:

profile(CM or HMM)

alignment

procedure

Test: How similar are these alignments?

no seed/test sequencepair is > 80% identical

80% id

sequenceidentity

tree

trusted “gold standard’alignment (152 sequences):

seed alignment(101 sequences):

test alignment(51 sequences)

Profiles produce accurate SSU alignments

alignment timeaccuracy (sec/seq)

Muscle-3.8.31 (de novo) 95.4% 0.49

HMMER3 (HMMs) 96.8% 0.04

Infernal 1.1 (CMs) 98.1% 0.50

Muscle: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.

HMMER: hmmer.janelia.org

Infernal: infernal.janelia.org

Probabilistic models allow direction calculation of useful quantities

• Posterior decoding algorithm computes the posterior probability that each nucleotide iscorrectly aligned given the model

– allows HMM banding for CM alignment (O(N3log(N)) reduced to close to O(N2)

– useful for identifying and removing (masking) columns that are not reliably alignedprior to phylogenetic inference

SSU tree

SSU alignment

SSU sequences

alignmentprogram



Mask columns

5ʼ

3ʼ

100

200

300

400

500

600

700

800

900

1000

1100

1200

1300

1400

1500

Phil Hugenholtz’s manually created mask imposed on archaeal SSUblack: included in alignment (1257) pink: excluded from alignment (251)


Secondary Structure: small subunit ribosomal RNA

Archaeoglobus fulgidus(X05567,AE000965)1.cellular organisms 2.Archaea 3.Euryarchaeota 4.Archaeoglobales 5.Archaeoglobaceae6.Archaeoglobus February 2001

5’

3’

Citation and related information available at http://www.rna.icmb.utexas.edu

AUUC U G G U

U GAUCCUGCCAGAG

GC

CG

CU

GC

U

AUC

CG

GC

UG

G

GAC

U AAG

CC AUGC

G

A

G U CA A

G G G G C U U G U A U C C C UUC

GGGGAUGCAAGCACCGGC

GG

ACGGC

UC

AGU

AACA

CGUGGAC A

ACC

UG

CCCUCGGG

U G G G GG A U A

A C C C C G G GAA

ACUGGGGCU

AAUCCCCC

AU

AG

GGGAUGGG

UACUG

GAAUGUCCCAUCUC

CG

AAAGCGC

UU A G C G

CCCGAGG

AU

GG

GUCUGCGGC

GGA

UU

AG

GUU

GUU

GG

UG

GGG

UAACG

G CC

CA

CC

AA

GC

CGAA G A

UC

CG

UA

CGGGCCAUG

AG A

GU GGG A

GC C C G G

AG

AUGGACC

CUGAGACA C G

G G U C C AGG

CC

CUA

C GG

GG

CG C A G

CAGGC

G

CGAAACC

UCCG

CAAUGCGGG

AA

A C C G C G A C G G G GUC

AG

CC

GG

AGUGCUCGCGCAUC G C G C G G G C

UG

UC

GG

GG

UG

CCUAA A A

AG

CA

CC

CC

ACA

GC

AA GGGCCGGGC

AA

G GCCGG

UGGCA

GCCGC C

GC G

GUAA

UA

CCGG

CGGCCCGA

GU

GG

CG

GC

CA

CUUUU

AU

UG G

GC

CUA

AA

GC

GUCCGUA

GCCGGGCUGGUA

AGUCCUCCGGGA

AAUCUGGCGGCU

UA A C C G U C A G

A C UG C C G G A G G A

U AC U G C C A G C C

UAG

GGACCGGGA

GA

GGCCGGG

GGUAUUCCCGGAGUA

GGGGUGA

A A U C CU

GU A

AUC C C G G G A G G A C C

AC C

UG

UGG C G

AA

GGCGCCCGGCUG

GAACGGGUCCGAC

GGUGAG

GGA C GA

AG

GCCAGGG

GA G

CGAACCGG

AUU

A G AUAC

CCGG

GUA

GU

CCUGGC U G

UAAA

CG

AUG C G G A C U A G

GU

GU

CA

CC

GA

AG

CU A C

GAG

CU

UC

GG

UG

GU

GC

CGGAG

GGA

AGC

CGUUA

AGUCCGC

CGCCU

G G GGA G U A

CG G C C G

CA

AGGCUGAAA

CUUAA

A G G A A U U G G C GG

G G G A G C ACU

A C A A CGGGU

GGAGCCUGCGGU

UUAAU

UG

GA

UUCAAC G C

CG

GGAA

G C U U ACCGGGGGAG

ACAGCG

GGAUG

AAGGUCGGGC

UGA

A GACCUUA CC A

G

A

C UAGCUG A GA

GG

UGGUGC

A UG

GCCGCCGUCA

GUUCGUACUG

UGAAGC

A

U

CCUG

UU

A AGU

CAGGC

AA C G A G C

GA G A

CC C G C G C C C C C A G U U G C C

A GC G G U U C C C U

UC

GGGGAAG

CCGGGCACA

CUGGGGG

G

A

CUGCCGGCG

CUAAGCCGGAGG

AAGGUGCGGG

CAACGGCAGGU C

CGU

AUGCCCC G

AA

UCCCCCGG

GC

UAC

ACGCGGGCUAC A A U

GG

CC

GG

GAC

A A U GG

GU

A CCG

A C CC

C G AAAG

GGG

UAG

GU

AAU

CC

CC

UAAAC

CC

GG

UCUAA

CC

UGGGAUCGAGGGC

UGC

AACUCGCCCUCGU

GAACC

UG

GAAUCCG

UAGUAAUCGCGCC U

CA

AAAUG

GC

GC

GG

UGA

AU

AC

GUCCC

UGCUCCUUGCA

CACACCGCCCG

UC

AAGCCACCC

GAGUGGGCCAGGGGCGAGGGGGUGGCCC

UAGGCCACCUUCGAGCCCAGGGUCCGCGA

GGGGGGCU

AAG

UCGU

AAC

A AG

G

U A G C C G U A G G GGA

AUCUGCGGCUGGAUCACCUCCUN


Aeropyrum pernix (str. K1)(AP000062)1.cellular organisms 2.Archaea 3.Crenarchaeota 4.Desulfurococcales 5.Desulfurococcaceae 6.Aeropyrum 7.Aeropyrum pernix February 2001

5’

3’


ACUC C G G U

U GAUCCUGCCGGAC

CC

GA

CC

GC

U

AUC

GG

GG

UA

G

GGC

U AAG

CC AUGG

G

A

G U CG A

A C G C C C C G C CGC

UGCGGGGCGUGGC

GG

ACGGC

UG

AGU

AACA

CGUGGCU A

ACC

UA

CCCUCGGG

A C G G GG A U A

A C C CC U

C G G GAA

ACUGGGGCU

AAUCCCCG

AU

AG

GCGGGGGGUGCCU

GGA

AGGGUCCUCCGC

CG

AAAG

GGGCCGCGGGGGG

UUA

U C GC C C G C G G U C C G

CCCGAGG

AU

GG

GGCUGCGGC

CCA

UCA

CGG

UA

GUU

GG

CG

GGG

UAAUG

G CC

CG

CC

AA

GC

CUAC G A

CG

GG

UA

GGGGCCGUG

AG A

GC GGG A

GC C C C C

AG

AUGGGCA

CUGAGACA A G

G G C C C AGG

CC

CUA

C GG

GG

CG C A C

CAGGC

G

CGAAAAC

UCCG

CAAUGCGGG

CA

A C C G U G A C G G G GCU

AC

CC

CG

AGUGCCCCCCUUG G G G G G G C

UU

UU

CC

CC

GC

UGUAA G U

AG

GC

GG

GG

GA

AU

AA GCGGGGGGC

AA

G A CUGG

UGUCA

GCCGC C

GC G

GUAA

UA

CCAG

CCCCGCGA

GC

GG

UC

GG

GG

UGCUU

AC

UG G

GC

CUA

AA

GC

GCCCGUA

GCCGGCUCGACA

AGUCCCCGCCUA

AAGCCCCGGGCU

CA A C C C G G G G

A GU G G C G G G G A

U AC U G U C G G G C

UAG

GGGGCGGGA

GA

GGCCGAG

GGUACUCCCGGGGUA

GGGGCGA

A A U C CA

UU A


AC C

AG

UGG C G

AA

GGCGCUCGGCUG

GAACGC GCCCGAC

GGUGAG

GGGC GA

AA

GCCGGGG

GA G

CGAACCGG

AUU

A G AUAC

CCGG

GUA

GU

CCCGGC U G

UAAA

CG

AUG C G G G C U A G

GU

GU

UG

GG

CG

GG

CG U G

CG

AGC

CC

GC

CC

AG

UG

CCG

CAG

GGA

AGC

CGUUA

AGCCCGC

CGCCU

G G GGA G U A

CG G C C G

CA

AGGCUGAAA

CUUAA


G G G A G C ACC

A C A A GGGGU

GGAGCCUGCGGC

UUAAU

UG

GA

GUCAAC G C

CG

GGAA

CC U C C

ACCGGGGGCG

AC

AG

CAGGAU

GA

CG

GC

CA

GGC

UGA

A GGC

CU

UG

CC C

G

A

C GCG

CU

G A GGGG

AGAUGC

A UG

GCCGUCGCCA

GCUCGUGCCG

UGAGGU

G

U

CCUG

UU

A AGU

CAGGC

AA C G A G C

GA G A

CC C C C G C C C C U A G U U G C C

A U CC C C G G G G C

GACCCGGGGGG

CACACUAGGGG

G

A

CUGCCGCCG

CUAAGGCGGAGG

AAGGAGGGGG

CAACGGCAGGU C

AGC

AUGCCCC U

AA

ACCCCCGG

GC

UGC

ACGCGGGCUAC A A U

GG

CG

GG

GAC

A G C GG

GUG C

CG

A C CC

C G AAAG

GGG

GAG

GC

AAU

CC

CU

CAAAC

CC

CG

CCUCA

GU

UGGGAUCGAGGGC

UGC

AACUCGCCCUCGU

GAACG

UG

GAAUCCC

UAGUAACCGCGCGU

CA

UCAUC

GC

GC

GG

UGA

AU

AC

GUCCC

UGCUCCUUGCA

CACACUGCCCG

UC

GCUCCACCC

GAGGGGGGAGGGGGUGAGGCCCUCUCCG

C CGGGAGGGGGUCGAACCCCCUCCCCCCGA

GGGGGGAG

AAG

UCGU

AAC

A AG

G


ACCUGCGGCUGGAUCACCUCNNN


Halobacterium sp.(AE004437)1.cellular organisms 2.Archaea 3.Euryarchaeota 4.Halobacteriales 5.Halobacteriaceae 6.HalobacteriumMarch 2001

5’

3’


AUUC C G G U

U GAUCCUGCCGGAG

GC

CA

UU

GC

U

AUC

GG

AG

UC

C

GAU

U UAG

CC AUGC

U

A

G U UG U

G C G G G U UUA

GACCCGCAGC

GG

AAAGC

UC

AGU

AACA

CGUGGCC A

AGC

UA

CCCUGUGG

A C G G GA A U A

C U C U C G G GAA

ACUGAGGCU

AAUCCCCG

AU

AA

CGCUUUGC

UCCUG

GAAGGGGCAAAGCC

GG

AAACGCU

CC

G G C GCCACAGG

AU

GC

GGCUGCGGU

CGA

UU

AG

GUA

GAC

GG

UG

GGG

UAACG

G CC

CA

CC

GU

GC

CCAU A A

UC

GG

UA

CGGGUUGUG

AG A

GC A AG A

GC C C G G

AG

ACGGAAU

CUGAGACA A G

A U U C C GGG

CC

CUA

C GG

GG

CG C A G

CAGGC

G

CGAAACC

UUUA

CACUGUACG

AA

A G U G C G A U A A G GGG

AC

UC

CG

AGUGUGAAGGCAUAGA G C C U U C A C

UU

UU

GU

AC

AC

CGUAA G G

UG

GU

GC

AC

GA

AU

AA GGACUGGGC

AA

G A CCGG

UGCCA

GCCGC C

GC G

GUAA

UA

CCGG

CAGUCCGA

GU

GA

UG

GC

CG

AUCUU

AU

UG G

GC

CUA

AA

GC

GUCCGUA

GCUGGCUGAACA

AGUCCGUUGGGA

AAUCUGUCCGCU

UA A C G G G C A G

G C GU C C A G C G G A

A AC U G U U C A G C

UUG

GGACCGGAA

GA

CCUGAGG

GGUACGUCUGGGGUA

GGAGUGA

A A U C CU

GU A

AUC C U G G A C G G A C C

GC C

GG

UGG C G

AA

AGCGCCUCAGGA

GAACGGAUCCGAC

A GUGAG

GGA C GA

AA

GCUAGGG

UC U

CGAACCGG

AUU

A G AUAC

CCGG

GUA

GU

CCUAGC U G

UAAA

CG

AUG U C C G C U A G

GU

GU

GG

CG

CA

GG

CU A C

GAG

CC

UG

CG

CU

GU

GC

CGUAG

GGA

AGC

CGAGA

AGCGGAC

CGCCU

G G GAA G U A

CG U C U G

CA

AGGAUGAAA

CUUAA


G G G A G C ACU

A C A A CCGGA

GGAGCCUGCGGU

UUAAU

UG

GA

CUCAAC G C

CG

GACA

U C U C ACCAGCCCCG

ACAGUAGUAAU

GA

CG

GU

CA

GGU

UGA

U GA

CC

UU

AC

C C GA

G

GCUA CUGA GAGG

AGGUGC

A UG

GCCGCCGUCA

GCUCGUACCG

UGAGGC

G

U

CCUG

UU

A AGU

CAGGC

AA C G A G C

GA G A

CC C G C A C U C C U A A U U G C C

A GC A G U A C C C U

UUGGGUA

GCUGGG

UACAUUAGGUG

G

A

CUGCCGCUG

CCAAAGCGGAGG

AAGGAACGGG

CAACGGUAGGU C

AGU

AUGCCCC G

AA

UGGGCUGG

GC

AAC

ACGCGGGCUAC A A U

GG

UC

GA

GAC

A A U GG

GAA G

CC

A C UC

C G AGAG

GAG

GCG

CU

AAU

CU

CCU

AAAC

UC

GA

UCGUA

GU

UCGGAUUGAGGGC

UGA

AACUCGCCCUCAU

GAAGC

UG

GAUUCGG

UAGUAAUCGCGUGU

CA

GCAGC

GC

GC

GG

UGA

AU

AC

GUCCC

UGCUCCUUGCA

CACACCGCCCG

UC

AAAUCACCC

GAGUGGGGUUCGGAUGAGGCCGGCA

U GCGCUGGUCAAAUCUGGGCUCCGCAA

GGGGGAUU

AAG

UCGU

AAC

A AG

G


AUCUGCGGCUGGAUCACCUCCU


Methanococcus vannielii(M36507)1.cellular organisms 2.Archaea 3.Euryarchaeota 4.Methanococcales 5.Methanococcaceae 6.Methanococcus February 2001

5’

3’

Citation and related information available at http://www.rna.ccbb.utexas.edu

AUUC C G G U

U GAUCCCGCCGGAG

GC

UA

CU

GC

U

AUU

GG

GG

UU

C

GAC

U AAG

CC AUGC

G

A

G U CU

A U G G U UUC

GGCCAUGGC

GG

ACGGC

UC

AUU

AACA

CGUGGUU A

ACU

UA

ACCUCAGG

U G G A GC A U A

A C C U U G G GAA

ACUGAGGAU

AAUUCUCC

AU

AAGAAAAGC

AG

UCUG

GAACGA

UUCUUUUC

UG

AAAGCA

UA

U G C GCCCGAGG

AU

AG

GACUGCGCU

CGA

UU

AG

GUA

GUU

GG

UG

GGG

UAAUG

G CC

CA

CC

AA

GC

CUAC G A

UC

GA

UA

CGGGCCUUG

AG A

GA GGG A

GC C C G G

AG

AUGGGGA

CUGAGACA C G

G C C C C AGG

CC

CUA

C GG

GG

CG C A G

CAGGC

G

CGAAACC

UCCG

CAAUGCACG

AA

A G U G C G A C G G G GGG

AC

CC

CA

AGUGCUCAUGCACA G C A U G G G C

UU

UU

AU

CA

AG

UGUAA A C

AG

CU

UG

AG

GA

AU

AA GGGCUGGGC

AA

G UUCGG

UGCCA

GCAGC C

GC G

GUAA

UA

CCGA

CGGCCCGA

GU

GG

UA

GC

CA

CUCUU

AU

UG G

GC

CUA

AA

GC

GUCCGUA

GCCGGUCCAGUA

AGUCCCUGUUUA

AAUUCUCUGGCU

UA A C C A G A G G

A CU G G C A G G G A

U AC U G C U G G A C

UUG

GGACCGGGA

GA

GGACAAG

GGUACUCCAGGGGUA

GCGGUGA

A A U G UG

UU G

AUC C U U G G A G G A C C

AC C

UA

UGG C G

AA

GGCACUUGUCUG

GAACGGGUCCGAC

GGUGAG

GGA C GA

AA

GCCAGGG

GC G

CGAACCGG

AUU

A G AUAC

CCGG

GUA

GU

CCUGGC C G

UAAA

CU

CUG C G A A C U A G

GU

GU

CA

CC

UG

GG

CC U C

GAG

CC

CA

GG

UG

GU

GC

CGAAG

GGA

AGC

CGUUA

AGUUCGC

CGCCU

G G GGA G U A

CG G U C G

CA

AGACUGAAA

CUUAA


G G G A G C ACC

A C A A CGGGU

GGAGCCUGCGGU

UUAAU

UG

GA

UUCAAC G C

CG

GGCA

U C U C ACCAGGAGCG

ACAGCA

UGAUG

ACGGCCAGGU

UGA

C GACCUUGCC U

G

A

A GCGCUGA GA

GG

UGGUGC

A UG

GCCAUCGUCA

GCUCGUACCG

CGAGGC

G

U

CCUG

UU

A AGU

CAGGU

AA C G A G C

GA G A

CC C G U G C C C U A U G U U G C G

A CU A C U U U C U

CC

GGAAGGUAAGCACU

CAUAGGG

G

A

CCGCUAGCG

CUAAGCUAGAGG

AAGGAGCGGG

CAACGAUAGGU C

CGC

AUGCCCC G

AA

UCUCCUGG

GC

UAC

ACGCGGGCUAC A A U

GG

CU

AG

GAC

A A U GG

GCU G

CU

A C CC

U G AAAA

GGG

ACG

CG

AAU

CU

CC

GAAAC

CU

AG

UCGUA

GU

UCGGAUCGUGGGC

UGU

AACUCGCCCACGU

GAAGC

UG

GAAUCCG

UAGUAAUCGCAGU U

CA

UAAUA

CU

GC

GG

UGA

AU

GU

GUCCC

UGCUCCUUGCA

CACACCGCCCG

UC

ACACCACCC

GAGUUGGGUUCAGGUGAGGCCUUGGCCU U U

GGCUAGGGUCGAACCUGGGCUCAGCGA

GGGGGGUG

AAG

UCGU

AAC

A AG

G


ACCUGCGGCUGGAUCACCUCCNN


Natronorubrum bangense(Y14028)1.cellular organisms 2.Archaea 3.Euryarchaeota 4.Halobacteriales 5.Halobacteriaceae 6.Natronorubrum May 2001

5’

3’


AUUC C G G U

U GAUCCUGCCGGAG

GU

CA

UU

GC

U

AUU

GG

AG

UC

C

GAU

U UAG

CC AUGC

U

A

G U UG U

A C G A G U UUG

UACUCGUAGC

AG

AUAGC

UC

AGU

AACA

CGUGGCC A

AAC

CA

CCCUAUGG

A U C C GG A U A

A C C U C G G GAA

ACUGAGGCC

AAUCCGGA

AU

AC

GAUUCCC

AA

GC

UG

GAACU

GC

UGGGAAUC

CG

AAACGCU

CA

G G C GCCAUAGG

AU

GU

GGCUGCGGC

CGA

UU

AG

GUA

GAC

GG

UG

GGG

UAACG

G CC

CA

CC

GU

GC

CAAU A A

UC

GG

UA

CGGGUUGUG

AG A

GC A AG A

GC C C G G

AG

ACGGUAU

CUGAGACA A G

A U A C C GGG

CC

CUA

C GG

GG

CG C A G

CAGGC

G

CGAAACC

UUUA

CACUGCACG

CC


AC

UC

CG

AGUGCGAGGGCAUAU A G U C C U C G C

UU

UU

CA

CC

AC

CGUAA G G

AG

GU

GG

UA

GA

AU

AA GUGCUGGGC

AA

G A CCGG

UGCCA

GCCGC C

GC G

GUAA

UA

CCGG

CAGCACGA

GU

GA

UG

AC

CG

CUAUU

AU

UG G

GC

CUA

AA

GC

GUCCGUA

GCUGGCCGUGCA

AGUCUAUCGGGA

AAUCUGUGUGCC

UA A C A C A C A G

G C GU C C G G U G G A

A AC U G C U C G G C

UUG

GGACCGGAA

GA

CCAGAGG

GGUACGUCUGGGGUA

GGAGUGA

A A U C CC

GU A


AC C

GG

UGG C G

AA

AGCGCCUCUGGA

AGACGGAUCCGAC

GGUGAG

GGA C GA

AA

GCUCGGG

UC A

CGAACCGG

AUU

A G AUAC

CCGG

GUA

GU

CCGAGC U G

UAAA

CG

AUG U C U G C U A G

GU

GU

GA

CA

CA

AA

CU A C

GAG

UU

UG

UG

UU

GU

GC

CGUAG

GGA

AGC

CGUGA

AGCAGAC

CGCCU

G G GAA G U A

CG U C C G

CA

AGGAUGAAA

CUUAA


G G G A G C ACU

A C A A CCGGA

GGAGCCUGCGGU

UUAAU

UG

GA

CUCAAC G C

CG

GACA

U C U C ACCAGCAUCG

ACAAUGU

GCAGUGA

CG

GU

CA

GUG

UGA

U GAG

CU

UA

CC U

GA

GCCA UUGA GAGG

AGGUGC

A UG

GCCGCCGUCA

GCUCGUACCG

UGAGGC

G

U

CCUG

UU

A AGU

CAGGC

AA C G A G C

GA G A

CC C G C A U G C C U A A U U G C C

A GC A G U A C C C U

UGUGGUA

GCUGGG

UACAUUAGGUA

G

A

CUGCCAGUG

CCAAACUGGAGG

AAGGAACGGG

CAACGGUAGGU C

AGU

AUGCCCC G

AA

UGUGCUGG

GC

GAC

ACGCGGGCUAC A A U

GG

CC

AC

GAC

A G U GG

GAU G

CA

A C CC

C G AAAG

GGG

ACG

CU

AAU

CU

CCG

AAAC

GU

GG

UCGUA

GU

UCGGAUUGAGGGC

UGA

AACUCGCCCUCAU

GAAGC

UG

GAUUCGG

UAGUAAUCGCGCC U

CA

GAAGG

GC

GC

GG

UGA

AU

AC

GUCCC

UGCUCCUUGCA

CACACCGCCCG

UC

AAAGCACCC

GAGUGAGGUCCGGAUGAGGCCGCCGC A A

CGGCGGUCGAAUCUGGGCUUCGCAA

GGGGGCUU

AAG

UCGU

AAC

A AG

G




Nanoarchaeum equitans(AJ318041)1.cellular organisms 2.Archaea 3.Nanoarchaeota 4.Nanoarchaeum July 2004

5’

3’


ACUC C C G U

U GAUCCUGCGGGAG

GC

CA

CC

GC

U

AUC

UC

CG

UC

C

GGC

U AAC

CC AUGG

A

A

G G CGA

G G G U C C C C G GGU

AAGGGGGCCCGCC

GC

ACGGC

UG

AGU

AACA

CGUCGGU A

ACC

UA

CCCUCGGG

A C G G GG

A U AA C C C C G G G

AA

ACUGGGGCU

AAUCCCCG

AU

AG

GGGAUGGGUGCUG

GAAGGCCCCAUCCC

CG

AGAGGGGCUAGCGGUAC

UUC C CC C G C U A G C C C G

CCCGAGG

AU

GG

GCCGGCGGC

CCA

UC

AG

GUA

GUU

GG

CG

GGG

UAAUG

G CC

CG

CC

AA

GC

CGAA G A

CG

GG

UA

GGGGCCGUG

AG A

GC GGGA

GC C C C C

AG

AUCGGCACUG

AGA

C A A GG G C C G A

GG

CC

CUA

C GG

GG

CG C A C

CAGGG

G

CGAAACC

UCCG

CAAUGCGGG

AA

A C C G U G A C G G G GGG

AC

GG

AG

AGUGCCGGAGGGCGUUA U G C U C U C C G G C

UU

UU

GG

GG

AG

UGUAA G U

AG

CU

CC

CC

GA

AU

AA GCGGUGGGC

AA

G A GGGG

UGGCA

GCCGC C

GC G

GGAA

CA

CCCC

CACCGCGA

GC

GG

UG

GC

CG

UGAUU

AU

UG G

GC

CUA

AA

GG

GGCCGUA

GCCGGGCCGGUG

UGGCUCCGGUGAAA

UCCUCGGGCU

CA A C C C G A G G

G C GC G C C G G A G C

U AC U A C C G G C C

UAG

GGACCGGGA

GG

GGCCGAC

CGUACUCCCGGGGGA

GCGGUGA

A A U G CU

GU A

AUC C C G G G A G G A C G

AC C

CG

UGG C G

AA

AGCGGUCGGCCA

GAACGGGUCCGAC

GGUGAG

GGCC GA

AG

GCCGGGG

GC U

AGAACGGG

AUU

A G AGAC

CCCG

GUA

UU

CCCGGC U G

UCAA

CG

CUG C G G G C U A C

CU

GC

UG

GG

CG

GG

CU A C

GAG

CC

CG

CC

CA

GU

GG

GGUAG

GGA

AGC

CGUUA

AGCCCGC

CGCCU

G G GGA G U A

CG G C C G

CA

AGGCUGAAA

CUUAA

A G G A A U A G G C GG

G G G A G C AC

A C A A GA GGU

GGGGUGCGCGGU

UUAAU

UG

GA

UUCGAC G C

CG

GGAA

C C U C ACCGGGGCUG

ACAGCA

CAAUGA

UG

GU

CG

GCC

UGA

A GGG

CC

UA

CC G

GA

G GCGCUGA GA

GG

AGGUGC

A UG

GCCGCCGUCA

GCCUGUGCCG

UGAGGU

G

C

CCUG

UU

A AGU

CAGGA

AA C A G G C

GA G A

CC C G C G C C C G C A G

U U GC G

A CG G C C G

AA

AGGCCGGCACA

CUGCGGG

G

A

CUGCCGGGG

AAACCCGGAGG

AAGGUGCGGG

CGACGGCAGGU A

UGC

AUGCCCC G

AA

UGCCCCGG

GC

UAC

ACGCGCGCAUC A A U

GG

GC

GG

GAC

A G GG

GGC

C GCG

A CC

CC

G AAA

GG

GGG

AGCAA

AUC

CCC

AAAC

CC

GC

UCUCA

GU

CCAGAUCGAGGGC

UGC

AACUCGCCCUCGU

GACGG

CG

GAAUCUC

UAGUAGUCGGACGU

CA

CCAGC

GU

CC

GG

CGA

AU

AC

GUCCC

UGCUCCUUGCA

CUCACCGCCCG

UC

AAGCCACCC

GAGCUGGGGCCUAGC

GAGGCCGUGGGGGGU

U CGCCCCCCACGGUCGA

GCUAGGCCCCGGCGA

GGGGGGCU

AAG

UCGA

CAC

A AG

G


ACCUGCGGCUGGAUCACCUCCUN


Natronobacterium innermongoliae(AF009601)1.cellular organisms 2.Archaea 3.Euryarchaeota 4.Halobacteriales 5.Halobacteriaceae 6.Natronobacterium February 2001

5’

3’


AUUC C G G U

U GAUCCUGCCGGAG

GU

CA

UU

GC

U

AUU

GG

AG

UC

C

GAU

U UAG

CC AUGC

U

A

G U UG U

A C G A G U UUA

GACUCGUAGC

AG

AUAGC

UC

AGU

AACA

CGUGGCC A

AAC

UA

CCCUAUGG

A U C C AG A C A

A C C U C G G GAA

ACUGAGGCU

AAUCUGGA

AU

AC

GACUCUC

AU

CCUG

GAGUGG

AGAGAGUC

CG

AAACGCU

CC

G G C GCCAUAGG

AU

GU

GGCUGCGGC

CGA

UU

AG

GUA

GAC

GG

UG

GGG

UAACG

G CC

CA

CC

GU

GC

CAGU A A

UC

GG

UA

CGGGUUGUG

AG A

GC A AG A

GC C C G G

AG

ACGGUAU

CUGAGACA A G

A U A C C GGG

CC

CUA

C GG

GG

CG C A G

CAGGC

G

CGAAACC

UUUA

CACUGCACG

CC


AC

UC

CA

AGUGCGAGGGCAUAU A G U C C U C G C

UU

UU

UG

CG

AC

CGUAA G G

UG

GU

CG

CG

GA

AU

AA GUGCUGGGC

AA

G A CCGG

UGCCA

GCCGC C

GC G

GUAA

UA

CCGG

CAGCACGA

GU

GA

UG

AC

CG

CUGUU

AU

UG G

GC

CUA

AA

GC

GUCCGUA

GCUGGCCGCGCA

AGUCUAUCGGGA

AAUCUCUUCGCU

UA A C G A A G A G

G C GU C C G G U G G A

A AC U G U G U G G C

UUG

GGACCGGAA

GA

CCAGAGG

GGUACGUCUGGGGUA

GGAGUGA

A A U C CC

GU A


AC C

GG

UGG C G

AA

AGCGCCUCUGGA

AGACGGAUCCGAC

GGUGAG

GGA C GA

AA

GCUCGGG

UC A

CGAACCGG

AUU

A G AUAC

CCGG

GUA

GU

CCGAGC U G

UAAA

CG

AUG U C U G C U A G

GU

GU

GA

CA

CA

GG

CU A C

GAG

CC

UG

UG

UU

GU

GC

CGUAG

GGA

AGC

CGUGA

AGCAGAC

CGCCU

G G GAA G U A

CG U C C G

CA

AGGAUGAAA

CUUAA


G G G A G C ACU

A C A A CCGGA

GGAGCCUGCGGU

UUAAU

UG

GA

CUCAAC G C

CG

GACA

U C U C ACCAGCAUCG

ACAAUGU

GCAGUGA

CG

GU

CA

GUG

UGA

U GAG

CU

UA

CC U

GA

GCCA UUGA GAGG

AGGUGC

A UG

GCCGCCGUCA

GCUCGUACCG

UGAGGC

G

U

CCUG

UU

A AGU

CAGGC

AA C G A G C

GA G A

CC C G C A C U C C U A A U U G C C

A GC A A C A C C C U

UGUGGUG

GUUGGG

UACAUUAGGAG

G

A

CUGCCAGUG

CCAAACUGGAGG

AAGGAACGGG

CAACGGUAGGU C

AGU

AUGCCCC G

AA

UGUGCUGG

GC

GAC

ACGCGGGCUAC A A U

GG

CC

AC

GAC

A G U GG

GAU G

CA

A C GC

C G AAAG

GCG

ACG

CU

AAU

CU

CC

GAAAC

GU

GG

UCGUA

GU

UCGGAUUGAGGGC

UGA

AACUCGCCCUCAU

GAAGC

UG

GAUUCGG

UAGUAAUCGCGCC U

CA

GAAGG

GC

GC

GG

UGA

AU

AC

GUCCC

UGCUCCUUGCA

CACACCGCCCG

UC

AAAGCACCC

GAGUGGGGUCCGGAUGAGGCCCGGU U U

CCGGGUCGAAUCUGGGCUCCGCAA

GGGGGCUU

AAG

UCGU

AAC

A AG

G




Pyrococcus abyssi(AJ248283)1.cellular organisms 2.Archaea 3.Euryarchaeota 4.Thermococcales 5.Thermococcaceae 6.Pyrococcus April 2001

5’

3’


CGUACUCCCUUAAUUC C G G U

U GAUCCUGCCGGAG

GC

CA

CU

GC

U

AUG

GG

GG

UC

C

GAC

U AAG

CC AUGC

G

A

G U CA A

G G G G G C G U C C C UUC

UGGGACGCCACCGGC

GG

ACGGC

UC

AGU

AACA

CGUCGGU A

ACC

UA

CCCUCGGG

A G G G GG A U A

A C C C C G G GAA

ACUGGGGCU

AAUCCCCC

AU

AG

GCCUGGGG

UACUG

GAAGGUCCCCAGGC

CG

AAAGGGAGCCG

UA

A G G C U C C GCCCGAGG

AU

GG

GCCGGCGGC

CGA

UU

AG

GUA

GUU

GG

UG

GGG

UAACG

G CC

CA

CC

AA

GC

CGAA G A

UC

GG

UA

CGGGCCGUG

AG A

GC GGG A

GC C C G G

AG

AUGGACA

CUGAGACA C G

G G U C C AGG

CC

CUA

C GG

GG

CG C A G

CAGGC

G

CGAAACC

UCCG

CAAUGCGGG

AA

A C C G C G A C G G G GGG

AC

CC

CC

AGUGCCGUGCCUCU G G C A C G G C

UU

UU

CC

GG

AG

UGUAA A A

AG

CU

CC

GG

GA

AU

AA GGGCUGGGC

AA

G GCCGG

UGGCA

GCCGC C

GC G

GUAA

UA

CCGG

CGGCCCGA

GU

GG

UG

GC

CA

CUAUU

AU

UG G

GC

CUA

AA

GC

GGCCGUA

GCCGGGCCCGUA

AGUCCCUGGCGA

AAUCCCACGGCU

CA A C C G U G G G

G C UC G C U G G G G A

U AC U G C G G G C C

UUG

GGACCGGGA

GA

GGCCGGG

GGUACCCCCGGGGUA

GGGGUGA

A A U C CU

AU A

AUC C C G G G G G G A C C

GC C

AG

UGG C G

AA

GGCGCCCGGCUG

GAACGGGUCCGAC

GGUGAG

GGCC GA

AG

GCCAGGG

GA G

CGAA

CCGG

AUU

A G AUAC

CCGG

GUA

GU

CCUGGC U G

UAAA

GG

AUG C G G G C U A G

GU

GU

CG

GG

CG

AG

CU U C

GAG

CU

CG

CC

CG

GU

GC

CGUAG

GGA

AGC

CGUUA

AGCCCGC

CGCCU

G G GGA G U A

CG G C C G

CA

AGGCUGAAA

CUUAA


G G G A G C ACU

A C A A GGGGU

GGAGCGUGCGGUUUAAU

UG

GA

UUCAAC

G CC

GGGAA

C C U C ACCGGGGGCG

ACGGCA

GGAUGA

AG

GC

CA

GGC

UGA

A GGU

CU

UG

CC G

GA

CGCGCCGA GA

GG

AGGUGC

A UG

GCCGCCGUCA

GCUCGUACCG

UGAGGC

G

U

CCAC

UU

A AGU

GUGGU

AA C G A G C

GA G A


A GU C C C U C C C G

CU

CGGGAGGGAGGCACU

CUGGGGG

G

A

CUGCCGGCG

AUAAGCCGGAGG

AAGGGGCGGG

CGACGGUAGGU C

AGU

AUGCCCC G

AA

ACCCCCGG

GC

UACACGCGCGCUAC A A U

GG

GC

GG

GAC

A A U GG

GUG C

CG

A C CC

C G AAAG

GGG

GAG

GU

AAU

CC

CCU

AAAC

CC

GC

CCUCA

GU

UCGGAUCGCGGGC

UGC

AACUCGCCCGCGU

GAAGC

UG

GAAUCCC

UAGUACCCGCGCGU

CA

UCAUC

GC

GC

GG

CGA

AU

AC

GUCCC

UGCUCCUUGCA

CACACCGCCCG

UC

ACUCCACCC

GAGCGGGGCCUAGGUGAGGCCCGAUCUCCU

U CGGGAGGUCGGGUCGAGCCUAGGCUCCGUGA

GGGGGGAG

AAG

UCGU

AAC

A AG

G


ACCUACGGCUCGAUCACCUCCUAUC


Pyrococcus furiosus(U20163)1.cellular organisms 2.Archaea 3.Euryarchaeota 4.Thermococcales 5.Thermococcaceae 6.Pyrococcus September 2000

5’

3’


AUUC C G G U

U GAUCCUGCCGGAG

GC

CA

CU

GC

U

AUG

GG

GG

UC

C

GAC

U AAG

CC AUGC

G

A

G U CA A


UGGGACGCCACCGGC

GG

ACGGC

UC

AGU

AACA

CGUCGGU A

ACC

UA

CCCUCGGG

A G G G GG A U A

A C C C C G G GAA

ACUGGGGCU

AAUCCCCC

AU

AGGCCUGGGG

UACUG

GAAGGUCCCCAGGCC

GA

AAGGGAGCCG

UA

A G G C C CG

CCCGAGG

AU

GC

GGCGGCGGC

CGA

UU

AG

GUA

GUU

GG

UG

GGG

UAACG

G CC

CA

CC

AA

GC

CGAA G A

UC

GG

UA

CGGGCCGUG

AG A

GC GGG A

GC C C G G

AG

AUGGACA

CUGAGACA C G

G G U C C AGG

CC

CUA

C GG

GG

CG C A G

CAGGC

G

CGAAACC

UCCG

CAAUGCGGG

AA


AC

CC

CC


UU

UU

CC

GG

AG

UGUAA A A

AG

CU

CC

GG

GA

AU

AA GGGCUGGGC

AA

G GCCGG

UGGC

AGC

CGC C

GC

GGUAA

UA

CCGG

CGGCCCGA

GU

GG

UG

GC

CA

CUAUU

AU

UG G

GC

CUA

AA

GC

GGCCGUA

GCCGGGCCCGUA

AGUCCCUGGCGA

AAUCCCACGGCU

CA A C C G U G G G



UUG

GGACCGGGA

GA

GGCCGGG

GGUACCCCCGGGGUA

GGGGUGA

A A U C CU

AU A


GC C

AG

UGG C G

AA

GGCGCCCGGCUG

GAACGGGUCCGAC

GGUGAG

CGCGGA

AG

GCCAGGG

GA G

CGAACCGG

AUU

A G AUAC

CCGG

GUA

GU

CCUGGC U G

UAAA

GG

AUG C G G G C U A G

GU

GU

CG

GG

CG

AG

CU U C

GAG

CU

CG

CC

CG

GU

GC

CGUAG

GGA

AGC

CGUUA

AGCCCGC

CGCCU

G G GGA G U A

CG G C C G

CA

AGGCUGAAA

CUUAA


G G G A G C ACU

A C A A GGGGU

GGAGCGUGCGGU

UUAAU

UG

GA

UUCAAC G C

CG

GGAA

C C U C ACCGGGGGCG

ACGGCAGGA

UG

AA

GG

CC

AG

GCU

GA

A GGU

CU

UG

CC G G

AC

GCGCCGA GA

GG

AGGUGC

A UG

GCCGCCGUCA

GCUCGUACCG

UGAGGC

G

U

CCAC

UU

A AGU

GUGGU

AA C G A G C

GA G A



CU

CGGGAGGAGGCACU

CUGGGGG

G

A

CUGCCGGCG

AUAAGCCGGAGG

AAGGGGCGGG

CGACGGUAGGU C

AGU

AUGCCCC G

AA

ACCCCCGG

GC

UAC

ACGCGCGCUAC A A U

GG

GC

GG

GAC

A A U GG

GAC C

CG

A C CU

C G AAAG

GGG

AAG

GG

AAU

CC

CC

UAAAC

CC

GC

CCUCA

GU

UCGGAUCGCGGGC

UGC

AACUCGCCCGCGU

GAAGC

UG

GAAUCCC

UAGUACCCGCGUGU

CA

UCAUC

GC

GC

GG

CGA

AU

AC

GUCCC

UGCUCCUUGCA

CACACCGCCCG

UC

ACUCCACCC

GAGCGGAGUCCGGGUGAGGCCUGAUCUCCU

U CGGGAGGUCAGGUCGAGCCCGGGCUCCGUGA

GGGGGGAG

AAG

UCGU

AAC

A AG

G

U A A C C G U A G G GGA

ACCUACGGCUCGAUCACCUCCUN


Pyrococcus horikoshii(AP000001)1.cellular organisms 2.Archaea 3.Euryarchaeota 4.Thermococcales 5.Thermococcaceae 6.Pyrococcus March 2001

5’

3’


AUUC C G G U

U GAUCCUGCCGGAG

GC

CA

CU

GC

U

AUG

GG

GG

UC

C

GAC

U AAG

CC AUGC

G

A

G U CA A


UGGGACGCCACCGGC

GG

ACGGC

UC

AGU

AACA

CGUCGGU A

ACC

UA

CCCUCGGG

A G G G GG A U A

A C C C C G G GAA

ACUGGGGCU

AAUCCCCC

AU

AG

GCCUGGG

GU

ACUG

GAAGGU

CCCCAGGC

CG

AAAGGGAGCCG

UA

A G G C U C C GCCCGAGG

AU

GG

GCCGGCGGC

CGA

UU

AG

GUA

GUU

GG

UG

GGG

UAACG

G CC

CA

CC

AA

GC

CGAA G A

UC

GG

UA

CGGGCCGUG

AG A

GC GGG A

GC C C G G

AG

AUGGACA

CUGAGACA C G

G G U C C AGG

CC

CUA

C GG

GG

CG C A G

CAGGC

G

CGAAACC

UCCG

CAAUGCGGG

AA


AC

CC

CC


UU

UU

CC

GG

AG

UGUAA A A

AG

CU

CC

GG

GA

AU

AA GGGCUGGGC

AA

G GCCGG

UGGCA

GCCGC C

GC G

GUAA

UA

CCGG

CGGCCCGA

GU

GG

UG

GC

CA

CUAUU

AU

UG G

GC

CUA

AA

GC

GGCCGUA

GCCGGGCCCGUA

AGUCCCUGGCGA

AAUCCCACGGCU

CA A C C G U G G G



UUG

GGACCGGGA

GA

GGCCGGG

GGUACCCCCGGGGUA

GGGGUGA

A A U C CU

AU A


GC C

AG

UGG C G

AA

GGCGCCCGGCUG

GAACGGGUCCGAC

GGUGAG

GGCC GA

AG

GCCAGGG

GAG

CGAACCGG

AUU

A G AUAC

CCGG

GUA

GU

CCUGGC U G

UAAA

GG

AUG C G G G C U A G

GU

GU

CG

GG

CG

AG

CU U C

GAG

CU

CG

CC

CG

GU

GC

CGUAG

GGA

AGC

CGUUA

AGCCCGC

CGCCU

G G GGA G U A

CG G C C G

CA

AGGCUGAAA

CUUAA


G G G A G C ACU

A C A A GGGGU

GGAGCGUGCGGU

UUAAU

UG

GA

UUCAAC G C

CG

GGAA

C C U C ACCGGGGGCG

ACGGCA

GGAUG

AAG

GC

CA

GGC

UGA

A GGU

CU

UG

CC G

GA

C GCGCCGA GA

GG

AGGUGC

A UG

GCCGCCGUCA

GCUCGUACCG

UGAGGC

G

U

CCAC

UU

A AGU

GUGGU

AA C G A G C

GA G A



CU

CGGGAGGGAGGCACU

CUGGGGG

G

A

CUGCCGGCG

AUAAGCCGGAGG

AAGGGGCGGG

CGACGGUAGGU C

AGU

AUGCCCC G

AA

ACCCCCGG

GC

UAC

ACGCGCGCUAC A A U

GG

GC

GG

GAC

A A U GG

GUG C

CG

A C CC

C G AAAG

GGG

GAG

GU

AAU

CC

CC

UAAAC

CC

GC

CCUCA

GU

UCGGAUCGCGGGC

UGC

AACUCGCCCGCGU

GAAGC

UG

GAAUCCC

UAGUACCCGCGCGU

CA

UCAUC

GC

GC

GG

CGA

AU

AC

GUCCC

UGCUCCUUGCA

CACACCGCCCG

UC

ACUCCACCC

GAGCGGGGCCUAGGUGAGGCCCGAUCUCCU

U CGGGAGGUCGGGUCGAGCCUAGGCUCCGUGA

GGGGGGAG

AAG

UCGU

AAC

A AG

G


ACCUACGGCUCGAUCACCUCCUAUC


Pyrodictium occultum(M21087)1.cellular organisms 2.Archaea 3.Crenarchaeota 4.Desulfurococcales 5.Pyrodictiaceae 6.Pyrodictium February 2001

5’

3’


ACUC C G G U

U GAUCCUGCCGGGC

CC

GA

CC

GC

U

AUC

GG

GG

UG

G

GAC

U AAG

CC AUGG

G

A

G U CG U

G C G C C C C C G GAC

GCGGGGGCGCGGC

GG

ACGGC

UG

AGU

AACA

CGUGGCC A

ACC

UA

CCCUCGGG

A C G G GG A U A

A C C C C G G GAA

ACUGGGGCU

AAUCCCCG

AU

AG

GCGAGGG

GG

CC

UG

GAACG

GG

UCCCUCGC

CG

AAAGGGCGCGCGGAG

CCU

C C C C G C G C G C C GCCCGAGG

AU

GG

GGCUGCGGC

CCA

UC

AG

GUA

GUU

GG

CG

GGG

UAACG

G CC

CG

CC

AA

GC

CGAU A A

CG

GG

UA

GGGGCCGUG

AG A

GC GGG A

GN C C C C

AG

AUGGGCA

CUGAGACA A G

G G C C C AGG

CC

CUA

C GG

GG

CG C A C

CAGGC

G

CGAAACC

UCCG

CAAUGCGGG

CA

A C C G U G A C G G G GUC

AC

CC

CG

AGUGCCGCCGAUA A G G C G G C

UG

UU

CC

CC

GC

UGUAG G A

AG

GC

GG

GG

GA

GU

AA GCGGGGGGC

AA

G UCUGG

UGUCA

GCCGC C

GC G

GUAA

UA

CCAG

CCCCGCGA

GC

GG

UC

GG

GA

UGAUU

AC

UG G

GC

CUA

AA

GC

GCCCGUA

GCCGGCCCGGUA

AGUCCCCCCCUA

AAGCCCCGGGCU

CA A C C C G G G G

A GU G G G G G G G A

U AC U G C C G G G C

UAG

GGGGCGGGA

GA

GGCCGAG

GGUACUCCCGGGGUA

GGGGCGA

A A U C CG

AU A


AC C

AG

UGG C G

AA

GGCGCUCGGCUG

GAACGC GCCCGAC

GGUGAG

GGGC GA

AA

GCCGGGG

GA G

CAAACCGG

AUU

A G AUAC

CCGG

GUA

GU

CCCGGC U G

UAAA

CG

AUG C G G G C U A G

GU

GU

UG

GG

CG

GG

CU U G

GAG

CC

CG

CC

CA

GU

GC

CGCAG

GGA

AGC

CGUUA

AGCCCGC

CGCCU

G G GGA G U A

CG G C C G

CA

AGGCUGAAA

CUUAA


G G N A G C ACC

A C A A GGGGU

GGAGCCUGCGGC

UUAAU

UG

GA

GUCAAC G C

CG

GGAA

U C U U ACCGGGGGCG

ACAGCA

GGAUG

ACG

GC

CA

GGC

UGA

C GAC

CU

UG

CC C

GA

CA

CGCUGA GA

GG

AGGUGC

A UG

GCCGUCGCCA

GCUCGUGCCG

UGAGGU

G

U

CCGG

UU

A AGU

CCGGC

AA C G A G C

GA G A

CC C C C A C C C C U A G U U G C U

A CC C C G G G G C

CACCCCGGGGG

CACACUAGGGG

G

A

CUGCCGNCG

UCC

AAGGCGGAGG

AAGGAGGGGG

CCACGGCAGGU C

AGC

AUGCCCC G

AA

UCCCCCGG

GC

UGC

ACGCGGGCUAC A A U

GG

CG

GG

GAC

A G C GG

GAU C

CG

A C CC

C G AAAG

GGG

GAG

GC

AAU

CC

CUU

AAAC

CC

CG

CCGCA

GU

UGGGAUCGAGGGC

UGC

AACUCGCCCUCGU

GAACG

CG

GAAUCCC

UAGUAACCGCGCGU

UA

GCAUC

GC

GC

GG

UGA

AU

AC

GUCCC

UGCUCCUUGCA

CACACCGCCCG

UC

GCUCCACCC

GAGCGGGGGAGGGGUGAGGCCCCGUCC

CU

C G CCA

GGGCGGGGUCGAACCUCUCCCCCGCGA

GGGGGGAG

AAG

UCGU

AAC

A AG

G


ACCUGCGGCUGGAUCACCUCCUN


Picrophilus torridus DSM 9790(AE017261)1.cellular organisms 2.Archaea 3.Euryarchaeota 4.Thermoplasmata 5.Thermoplasmatales 6.Picrophilaceae 7.Picrophilus 8.Picrophilus torridus July 2004

5’

3’


ACUC C G G U

U GAUCCUGCCGGCG

GC

CA

CU

GC

U

AUC

AA

GU

UC

C

GAC

U AAG

CC AUGC

G

A

G U CAA

G G G G C C GUA

AGGCACCGGC

GU

ACCGC

UC

AGU

AACA

CGCGGAU A

AUC

UA

CCCUCGGG

A A G G GC

A UAA C C U C G G G

AA

ACUGAGGCU

AAUU

CCCUAU

AG

CCAUUCA

GAACUG

GAAUGUUUGGAUGG

UG

AAGGCU

CC

G G C GCCCGGGG

AU

GA

GUCUGCGGC

CUA

UC

AG

GUA

GUA

GG

UG

GUG

UAACG

G AC

CA

CC

UA

GC

CUAA G A

CG

GG

UA

CGGGCCCUG

GG A

GGGGU A

GC C C G G

AG

AUGGACUCUG

AGA

C A C UA G U C C A

GG

CC

CUA

C GG

GG

CG C A G

CAGGC

G

CGAAACC

UGUG

CAAUGCGCG

CA

A G C G C G A C A C G GGG

AG

CU

UG

AGUGUCUUGGCAAA

A G C C A A G A CU

UU

UC

UU

AU

GCC

UAA A A

AG

CA

UA

AG

GA

AU

AA GGGCUGGGU

AA

G A CGGG

UGCCA

GCCGC C

GC G

GUAA

CA

CCCG

CAGCUCAA

GU

GG

UG

GU

CA

CUUUU

AC

UG A

GC

CUA

AA

GC

GUUCGUA

GCCGGCUUUGUA

AAUCUCCAGGUA

AAUUCUAGCGCU

UA A C G U U A G A

U CU C C U G G A G A

G AC U G C A A A G C

UUG

GGACCGGGU

GG

GGUUGAA

CGUACUUUCAGGGUA

GGGGUAA

A A U C CU

GU A

AUC C U G G A A G G A C G

AC C

GG

UAG C G

AA

GGCGUUCAACUA

GAACGGAUCCGAC

GGUGAG

GA A C GA

AG

GCUAGGG

GA G

CAAACCGG

AUU

A G AUAC

CCGG

GUA

GU

CCUAGC U G

UAAA

CU

CUG C C C A C U U G

GU

GU

UG

CC

UU

UC

CG U U

GAG

GG

GA

GG

CA

GU

GC

CGGAG

CGA

AGG

UGUUA

AGUGGGC

CGCUU

G G GGA G U A

UG G U C G

CA

AGACUGAAA

CUUAA


G G G A G C ACC

G C A A CGGGA

GGAAUGUGCGGU

UUAAU

UG

GA

UUCAAC G C

CG

GAAA

A C U C ACCGGGAGCG

ACCUGU

GGAUGA

GA

GU

CA

ACC

UGA

C GAG

UU

UA

CU C

GA

U AGCA GGA GA

GG

UGGUGC

A UG

GCCGUCGUCA

GCUCGUACCG

UAGGGC

G

U

UCAC

UU

A AGU

GUGA U

AA C G A G C

GA G A

CC C C C A U C U C C A A U U G C A

A UU A C C U A C G

CG

GGUAGGUAAGCACU

UUGGAGA

G

A

CCGCCAGCG

CUAAGCUGGAGG

AAGGAGGGGU

CGACGGCAGGUCA

GUACGCCCC G

AA

UCUCCCGG

GC

UAC

ACGCGCAUUAC A A A

GG

GC

AG

GAC

A A U GC

GU

U GCA

A CC

UC

G AAA

GG

GGAAG

CU

AAU

CG

CC

AAAC

CU

GU

CCGUA

GU

UAGGAUUGAGGGC

UGU

AACUCGCCCUCAU

GAAUC

UG

GAUUCCG

UAGUAAUCGCGGGU

CA

ACAAC

CC

GC

GG

UGA

AU

AU

GCCCC

UGCUCCUUGCA

CACACCGCCUG

UC

AAACCAUCC

GAGCUGGUGUUGGAU

GAGGGUUAGCUCG

A GAGGGUUAGCUCAA

AUCUGAUGUCAGUGA

GGAGGGUU

AAG

UCA U

AAC

A AG

G

U A U C U G U A G G GGA

ACCUGCAGAUGNNNNNNNNNNNN


Sulfolobus solfataricus(X03235)1.cellular organisms 2.Archaea 3.Crenarchaeota 4.Sulfolobales 5.Sulfolobaceae 6.Sulfolobus February 2001

5’

3’


AUUC C G G U

U GAUCCUGCCGGAC

CC

GA

CC

GC

U

AUC

GG

GG

UA

G

GGA

U AAG

CC AUGG

G

A

G U CU U

A C A C U C C C G GGU

AAGGGAGUGUGGC

GG

ACGGC

UG

AGU

AACA

CGUGGCU A

ACC

UA

CCCUCGGG

A C G G GG A U A

A C C C C G G GAA

ACUGGGGAU

AAUCCCCG

AU

AG

GGAAGGA

GU

CCUG

GAAUGG

UUCCUUCC

CU

AAAGGGCUAUAGGC

UAUUU

C C CG U U U G U A G C C G

CCCGAGG

AU

GG

GGCUACGGC

CCA

UC

AG

GCU

GUC

GG

UG

GGG

UAAAG

G CC

CA

CC

GA

AC

CUAU A A

CG

GG

UA

GGGGCCGUG

GA A

GC GGG A

GC C U C C

AG

UUGGGCA

CUGAGACA A G

G G C C C AGG

CC

CUA

C GG

GG

CG C A C

CAGGC

G

CGAAACG

UCCC

CAAUGCGCG

AA

A G C G U G A G G G C GCU

AC

CC

CG

AGUGCCUCCGCA

A G G A G G CU

UU

UC

CC

CG

CUC

UAA A A

AG

GC

GG

GG

GA

AU

AA GCGGGGGGC

AA

G UCUGG

UGUCA

GCCGC C

GC G

GUAA

UA

CCAG

CUCCGCGA

GU

GG

UC

GG

GG

UGAUU

AC

UG G

GC

CUA

AA

GC

GCCUGUA

GCCGGCCCACCA

AGUCGCCCCUUA

AAGUCCCCGGCU

CA A C C G G G G A

A CU G G G G G C G A

U AC U G G U G G G C

UAG

GGGGCGGGA

GA

GGCGGGG

GGUACUCCCGGAGUA

GGGGCGA

A A U C CU

UA G

AUA C C G G G A G G A C C

AC C

AG

UGG C G

GA

AGCGCCCCGCUA

GAACGC GCCCGAC

GGUGAG

A GGC GA

AA

GCCGGGG

CA G

CAAACGGG

AUU

A G AUAC

CCCG

GUA

GU

CCCGGC U G

UAAA

CG

AUG C G G G C U A G

GU

GU

CG

AG

UA

GG

CU U A

GAG

CC

UA

CU

CG

GU

GC

CGCAG

GGA

AGC

CGUUA

AGCCCGC

CGCCU

G G GGA G U A

CG G U C G

CA

AGACUGAAA

CUUAA


G G G A G C ACC

A C A A GGGGU

GGAACCUGCGGC

UCAAU

UG

GA

GUCAAC G C

CU

GGAA

U C U U ACCGGGGGAG

ACCGCA

GUAUGA

CG

GC

CA

GGC

UAA

C GAC

CU

UG

CC U

GA

C UCGCGGA GA

GG

AGGUGC

A UG

GCCGUCGCCA

GCUCGUGUUG

UGAAAU

G

U

CCGG

UU

A AGU

CCGGC

AA C G A G C

GA G A

CC C C C A C C C C U A G U U G G U

A UU C U G G A C U

CC

GGUCCAGAACCACA

CUAGGGG

G

A

CUGCCGGCG

UAAGCCGGAGG

AAGGAGGGGG

CCACGGCAGGU C

AGC

AUGCCCC G

AA

ACUCCCGG

GC

CGC

ACGCGGGUUAC A A U

GG

CA

GG

GAC

A A C GG

GAU G

CU

A C CU

C G AAAG

GGG

GAG

CC

AAU

CCU

UAAAC

CC

UG

CCGCA

GU

UGGGAUCGAGGGC

UGA

AACCCGCCCUCGU

GAACG

AG

GAAUCCC

UAGUAACCGCGGGU

CA

ACAAC

CC

GC

GG

UGA

AU

AC

GUCCC

UGCUCCUUGCA

CACACCGCCCG

UC

GCUCCACCC

GAGCGCGAAAGGGGUGAGGUCCCUUGC

GA U A

AGUGGGGGAUCGAACUCCUUUCCCGCGA

GGGGGGAG

AAG

UCGU

AAC

A AG

G


ACCUGCGGCUGGAUCACCUCNNN


Thermoplasma acidophilum (AL445067, M38637)1.cellular organisms 2.Archaea 3.Euryarchaeota 4.Thermoplasmales 5.Thermoplasmaceae 6.Thermoplasma July 2004

5’

3’


ACUC C G G U

C GAUCCUGCCGGCG

GU

CA

CU

GC

U

AUC

AG

GU

UC

C

GAC

U AAG

CC AUGC

A

A

G U CA U

G G G G C C GUA

AGGCACCGGC

GA

ACAGC

UC

AGU

AACA

CGUGGAU A

AUU

UA

CCCUCAGG

C G G G GC A U A

A C C U C G G GAA

ACUGAGGCU

AAUUCCCC

AU

AG

UCAUUAC

AAAC

UG

GAAUG

GUUGUAAUGA

UG

AAAGCU

UC

U G C ACCUGAGG

AU

AA

GUCUGCGGC

CUA

UC

AG

GUA

GUA

GG

UG

GUG

UAAAG

G AC

CA

CC

UA

GC

CUAA G A

CG

GG

UA

CGGGCCCUG

AA A

GGGGG A

GC C C G G

AG

AUGGACUCUG

AGA

C A A CA G U C C A

GG

CC

CUA

C GG

GG

CG C A G

CAGGC

G

CGAAAAC

UGUG

CAAUGCGCG

AA

A G C G C G A C A C G GGG

AG

CC

UG

AGUGCCUUGACUUUU U G U C A A G G C

UU

UU

CU

GA

UG

CCUAA A A

AG

CA

UC

AG

GA

AU

AA GGGCUGGGC

AA

G A CGGG

UGCCA

GCCGC C

GC G

GUAA

CA

CCCG

CAGCUCGA

GU

GG

UG

AU

CA

CUUUU

AU

UG A

GU

CUA

AA

GC

GUUCGUA

ACCGGUCUUAUA

AAUCUUCAGAUA

AAUUCUUCCGCU

UA A C G G A A G A

A CU U C U G A A G A

G AC U G U A A G A C

UUG

GGACCGGGU

GA

GGUUGAA

UGUACUUUCAGGGUA

GGGGUAA

A A U C CU

GU A

AUC C U G A A A G G A C G

AC C

GG

UGG C G

AA

AGCGUUCAACUA

GAACGGAUCCGAC

GGUGAG

GGA C GA

AG

GCUAGGG

GA G

CAAACCGG

AUU

A G AUAC

CCGG

GUA

GU

CCUAGC U G

UAAA

CG

CUG C C C A C U U G

GU

GU

UG

CU

UC

UC

CG U U

GAG

GG

GG

GG

CA

GU

GC

CGUAG

CGA

AGG

UGUUA

AGUGGGU

CACUU

G G GGA G U A

CG G C C G

CA

AGGCUGAAA

CUUAA


G G G A G C ACC

G C A A CGGGA

GGAGCGUGCGGU

UUAAU

UG

GA

UUCAAC G C

CG

GAAA

A C U C ACCGGGAGCG

ACCUUC

GGAUGA

GG

GU

CA

ACC

UGA

C GAA

UU

UA

CC C

GA

U AGA A GGA GA

GG

UGGUGC

A UG

GCCGUCGUCA

GCUCGUACCG

UAGGGC

G

U

UCAC

UU

A AGU

GUGA U

AA C G A G C

AA G A

CC C C C A U C U C U A A U U G C C

A GA C U G U C U U

UG

CGGGCAGAGGCACU

UUAGAGG

G

A

CCGCCAGCG

CUAAGCUGGAGG

AAGGAGGGGU

CGACGGCAGGUCA

GUACGCCCC G

AA

UCUCCCGG

GC

UAC

ACGCGCGCUAC A A A

GG

AC

GG

GAC

A A U GA

GUU G

CA

A CC

UC

G AAAG

GG

GA

AGCU

AAC

CU

CG

AAAC

CC

GU

UCGUA

GU

CAGGACUGAGGGC

UGU

AACUCGCCCUCAC

GAAUG

UG

GAUUCCG

UAGUAAUCGUAGGU

CA

ACAGC

CU

AC

GG

UGA

AU

AU

GCCCC

UGCUCCUUGCA

CACACCGCCCG

UC

AAACCAUCC

GAGCUGGUGUUGGAU

GAGGGUCCGUCCU C U

GGAUGGAUUCGA

AUCUGAUGUCAGUGA

GGAGGGUU

AAG

UCGU

AAC

A AG

G

U A U C C G U A G G GGA

ACCUGCGGAUGGAUCACCUCCNN


Thermococcus celer(M21529)1.cellular organisms 2.Archaea 3.Euryarchaeota 4.Thermococcales 5.Thermococcaceae 6.Thermococcus July 2004

5’

3’


AUUC C G G U

U GAUCCUGCCGGAG

GC

CA

CU

GC

U

AUG

GG

GG

UC

C

GAC

U AAG

CC AUGC

G

A

G U CA U

G G G G C G C C UU

GCGCGCACCGGC

GG

ACGGC

UC

AGU

AACA

CGUCGGU A

ACC

UA

CCCUCGGG

A G G G GG A U A

A C C C C G G GAA

ACUGGGGCU

AAUCCCCC

AU

AG

GCCUGAGG

UACUG

GAAGGUCCUCAGGC

CG

AAAGGGGCU

CU G C C C G

CCCGAGG

AU

GG

GCCGGCGGC

CGA

UU

AG

GUA

GUU

GG

UG

GGG

UAACG

G CC

CA

CC

AA

GC

CGAA G A

UC

GG

UA

CGGGCCAUG

AG A

GU GGG A

GC C C G G

AG

AUGGACA

CUGAGACA C G

G G U C C AGG

CC

CUA

C GG

GG

CG C A G

CAGGC

G

CGAAACC

UCCG

CAAUGCGGG

CA


AC

CC

CC

AGUGCCGUGGCAAC G C C A C G G C

UU

UU

CC

GG

AG

UGUAA A A

AG

CU

CC

GG

GA

AU

AA GGGCUGGGC

AA

G GCCGG

UGGCA

GCCGC C

GC G

GUAA

UA

CCGG

CGGCCCGA

GU

GG

UG

GC

CG

CUAUU

AU

UG G

GC

CUA

AA

GC

GUCCGUA

GCCGGGCCCGUA

AGUCCCUGGCGA

AAUCCCACGGCU

CA A C C G U G G G

G C UU G C U G G G G A


UUG

GGACCGGGA

GA

GGCCGGG

GGUACCCCUGGGGUA

GGGGUGA

A A U C CU

AU A

AUC C C A G G G G G A C C

GC C

AG

UGG C G

AA

GGCGCCCGGCUG

GAACGGGUCCGAC

GGUGAG

GGA C GA

AG

GCCAGGG

GA G

CGAACCGG

AUU

A G AUAC

CCGG

GUA

GU

CCUGGC U G

UAAA

GG

AUG C G G G C U A G

GU

GU

CG

GG

CG

AG

CU U C

GAG

CU

CG

CC

CG

GU

GC

CGAAG

GGA

AGC

CGUUA

AGCCCGC

CGCCU

G G GGA G U A

CG G C C G

CA

AGGCUGAAA

CUUAA


G G G A G C ACU

A C A A GGGGU

GGAGCGUGCGGU

UUAAU

UG

GA

UUCAAC G C

CG

GGAA

C C U C ACCGGGGGCG

ACGGCA

GGAUGA

AG

GC

CA

GGC

UGA

A GGU

CU

UG

CC G

GA

CACGCCGA GA

GG

AGGUGC

A UG

GCCGCCGUCA

GCUCGUACCG

UGAGGC

G

U

CCAC

UU

A AGU

GUGGU

AA C G A G C

GA G A


A GU C C U U C C C G

CUGGGGAGGAGG

CACUCUGGGGG

G

A

CCGCCGGCG

AUAAGCCGGAGG

AAGGAGCGGG

CGACGGUAGGU C

AGU

AUGCCCC G

AA

ACCCCCGG

GC

UAC

ACGCGCGCUAC A A U

GG

GC

GG

GAC

A A U GG

GAU C

CG

A CC

CC

G AAA

GG

GGA

AGGG

AAU

CC

CC

UAAAC

CC

GC

CCCCA

GU

UCGGAUCGCGGGC

UGC

AACUCGCCCGCGU

GAAGC

UG

GAAUCCC

UAGUACCCGCGUGU

CA

UCAUC

GC

GC

GG

CGA

AU

AC

GUCCC

UGCUCCUUGCA

CACACCGCCCG

UC

ACUCCACCC

GAGCGGGGUCCGGAU

GAGGCCUGAUCUCCCU

U CGGGGAGGUCGGGUCGA

GUCUGGGCUCCGUGA

GGGGGGAG

AAG

UCGU

AAC

A AG

G


ACCUACGGCUCGAUCACCUCCUN


Thermoproteus tenax(M35966)1.cellular organisms 2.Archaea 3.Crenarchaeota 4.Thermoproteales 5.Thermoproteaceae 6.Thermoproteus February 2001

5’

3’


AAAC C G G U

U GAUCCUGCCGGAC

CU

GA

CC

GC

U

AUC

GG

GG

UG

G

GGC

U AAG

CC AUGC

G

A

G U CG C

G C G C C C G G GGC

GCCGGGCGCGGC

GC

ACGGC

UC

AGU

AACA

CGUACCC A

ACC

UA

ACCUCGGG

A G G G GG A C A

A C C C C G G GAA

ACUGGGGCU

GAUCCCCC

AU

AG

GGGAAGG

GC

GCUG

GAAGGC

CCCUUCCU

CC

AAAGGGAUCGCGGGCG

AU

C U C C C G C G G U C C GCCCGAGG

GU

GG

GGGUACGGC

CCA

UC

AG

GUU

GUU

GG

CG

GGG

UAACG

G CC

CG

CC

AA

GC

CGAA G A

CG

GG

UA

GGGGCGGUG

AG A

GC C GU GA

GC C C C G

AG

AUGGGCA

CUGAGACA A G

G G C C C AGG

CC

CUA

C GG

GG

UG C A G

CAGGC

G

CGAAUAC

UCCG

CAAUGCGGG

CA

A C C G C G A C G G G GCC

AC

CC

CG

AGUGCCGGGCGAAGA G C C C G G C

UU

UU

GC

CC

GG

UGUAA G G

AG

CC

GG

GC

GA

AU

AA GCGGGGGGU

AA

G UCUGG

UGUCA

GCCGC C

GC G

GUAA

UA

CCAG

CCCCGCGA

GU

GG

UC

AG

GG

UGAUU

AC

UG G

GC

UUA

AA

GC

GCCCGUA

GCCGGCCCGGCA

AGUCGCUCCUGA

AAUCCCCAGGCU

CA A C C U G G G G

G CA G G G G G C G A

U AC U G C C G G G C

UAG

GGGGCGGGA

GA

GGCCGCC

GGUACUCCGGGGGUA

GGGGCGA

A A U C CU

AU A

AUC C C C G G A G G A C C

AC C

AG

UGG C G

AA

AGCGGGCGGCCA

GAACGC GCCCGAC

GGUGAG

GGGC GA

AA

GCCGGGG

GA G

CAAAGGGG

AUU

A G AUAC

CCCU

GUA

GU

CCCGGC C G

UAAA

CG

AUG C G G G C U A G

CU

GU

CG

GC

CG

GG

CU U A

GGG

CC

CG

GC

CG

GU

GG

CGUAG

GGA

AAC

CGUUA

AGCCCGC

CGCCU

G G GGA G U A

CG G C C G

CA

AGGCUGAAA

CUUAA


G G G G G C ACC

A C A A GGGGU

GAAGCUUGCGGC

UUAAU

UG

GA

GUCAAC G C

CG

GAAA

C C U U ACCCGGGGCG

ACAGCA

GGAUGA

AG

GC

CA

GGC

UAA

C GAC

CU

UG

CC G

GA

C GAGCUGA GA

GG

AGGUGC

A UG

GCCGUCGUCA

GCUCGUGCCG

UGAGGU

G

U

CCGG

UU

A AGU

CCGGC

AA C G A G C

GA G A

CC C C C A C C C C U A G U U G C U

A CC C C G C U C U

UC

GGGGCGGGGGCACA

CUAGGGG

G

A

CUGCCGGCG

UAAGCCGGAGG

AAGGAGGGGG

CGACGGCAGGU C

AGU

AUGCCCC G

AA

ACCCCGGG

GC

UGC

ACGCGAGCUGC A A U

GG

CG

GG

GAC

A G C GG

GAU C

CG

A C CC

C G AAAG

GGG

GAG

GC

AAU

CC

CG

UAAAC

CC

CG

CCCCA

GU

AGGGAUCGAGGGC

UGC

AACUCGCCCUCGU

GAACG

UG

GAAUCCC

UAGUAACCGCGUGU

CA

CCAAC

GC

GC

GG

UGA

AU

AC

GUCCC

UGCCCCUUGCA

CACACCGCCCG

UC

GCACCACCC

GAGGGAGUUCUCUGCGAGGCCCCUCGCUUGGGG

C AACCCAGGUGGGGGGACGAGCAGAGAACUCCCGA

GGGGGGUG

AAG

UCGU

AAC

A AG

G


ACCUGCGGCUGGAUCACCUCCNN

5ʼ

3ʼ

100

200

300

400

500

600

700

800

900

1000

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1200

1300

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1500



5ʼ

3ʼ

100

200

300

400

500

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700

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900

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1300

1400

1500

Posterior probability based archaeal SSU maskblack: included in alignment (1376)blue: excluded from alignment (132)


5ʼ

3ʼ

100

200

300

400

500

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1000

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1300

1400

1500


5ʼ

3ʼ

100

200

300

400

500

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5ʼ

3ʼ

100

200

300

400

500

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800

900

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1300

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1500

Comparison of manual and posterior-probability-based masksblack: included in both alignment (1216)

pink: excluded only from manual mask (160)blue: excluded only from PP mask (41)grey: excluded from both masks (91)


5ʼ

3ʼ

100

200

300

400

500

600

700

800

900

1000

1100

1200

1300

1400

1500


Probability-based mask colored by deletion frequencygrey: zero to very few deletions (1370/1376)blue: few deletions ...... red: many deletions

circles indicate excluded positions

5ʼ

3ʼ

100

200

300

400

500

600

700

800

900

1000

1100

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1300

1400

1500


Automated masking removes the majority of alignment errors

alignment timeaccuracy (sec/seq)

Muscle-3.8.31∗ 95.4% 0.49

HMMER3 (HMMs) 96.8% 0.04

Infernal 1.1 (CMs) 98.1% 0.50

Infernal 1.1 (CMs)posterior probability masked 99.5% 0.50

(1302/1530 columns)

Infernal produces alignment that are

very similar to manually refined alignments.

SSU-ALIGN: structural alignment of SSU rRNAs using CMs

known tree plusnew sequences

new sequences aligned

new SSU sequences

SSU-ALIGN



existing, known referenceSSU alignment and tree- accurate: because alignment errors confound

Goals of the alignment program:- accurate: because alignment errors confound phylogenetic inference- scalable to handle up to millions of seqs and fast:

SSU-ALIGNIncludes Infernal CMs for archaeal, bacterialand eukaryotic SSU rRNA accurate:- structural alignment of sequences- probabilistic masking of ambiguous columns

scalable and fast:- can generate alignment of millions of seqs- speed is about 1 second/full length sequence- easily parallelized on clusters SSU-ALIGN tutorial tomorrow at 10:30

Acknowledgements

Sean EddyElena RivasTravis WheelerTom JonesDiana KolbeSeolkyoung JungRob FinnJody ClementsFred DavisLee HenryMichael Farrar

eric nawrocki sean eddy’s labtandy/nawrocki-symposium.pdftree building program. de novo multiple...

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