Bioinformaatika arvestus ül (0)

5 VÄGA HEA

Kristina Raud
YAGB -41
060290
10.04.07

Bioinformaatika ülesanded

Fülogeneetilised puud.

DNA järjestuste fülogeneetiliste puude käsitsi koostamine kasutades kaugusmeetodeid (UPGMA, NJ).

Moodustada antud 5 järjestuse kaugusmaatriks ning joonistada kvantitatiivne juurtega fülogeneetiline puu kasutades UPGMA meetodit.
1 ACAAACAGTT CGATCGATTT GCAGTCTGGG
2 ACAAACAGTT TCTAGCGATT GCAGTCAGGG
3 ACAGACAGTT CGATCGATTT GCAGTCTCGG
4 ACTGACAGTT CGATCGATTT GCAGTCAGAG
5 ATTGACAGTT CGATCGATTT GCAGTCAGGA
Vastus:
A
B
C
D
B
9
C
2
11
D
4
11
4
E
5
12
5
3
AC
B
D
B
10
D
4
11
E
5
12
3
AC
B
B
10
DE
4,5
11,5
ACDE
B
10,75

Koostada eelpool toodud järjestuste fülogeneetiline puu kasutades Neighbour Joining meetodit.
Vastus:
A
B
C
D
B
9
C
2
11
D
4
11
4
E
5
12
5
3
r(A)=9+2+4+5=20
r(B)=9+11+11+12=43
r(C)=2+11+4+5=22
r(D)=4+11+4+3=22
r(E)=5+12+5+3=25
n=5

M

A
B
C
D
B
-12
C
2-14= -12
11-21,7= -10,7
D
4-14= -10
11-21,7= -10,7
4-14,7= -10,7
E
5-15= -10
12-22,7= -10,7
5-15,7= -10,7
3-15,7= -12,7
Teiste terminaalsete punktide vahekaugused:
dAU =(dAD+dEA - dDE)/2=3
dBU=(dBD+dBE-dDE)/2=10
dCU=(dCD+dCE-dDE)/2=3
d
A
B
C
B
9
C
2
11
U
3
10
3
Järgmine kaugusmaatriks:
r(A)=9+2+3=14
r(B)=9+11+10=30
r(C)=2+11+3=16
r(U)=3+10+3=16
n=4

M

A
B
C
B
9-22=-13
C
2-15= -13
11-23=-12
U
3-15= -12
10-23=-13
3-16=-13
dBU1=(dBA+dBC-dAC)/2=9
dUU1=(dUA+dUC-dAC)/2=2
d
AC (U1)
B
B
9
U
2
10
Järgmine kaugusmaatriks:
r(U1)=9+2=11
r(B)=9+10=19
r(U)=2+10=12
n=3
M
AC (U1)
B
B
9-30=-21
U
2-23=-21
10-31= -21
dU1U2=(dU1B+dU1U-dBU):2=(11-10)/2=0,5
AC (U1)
BU (U2)
0,5

Valida 4 järjestust (ülevalt) ja leida informatiivsed positsioonid (ML meetod). Koostada kõik võimalikud sugupuud (ML meetod) kasutades ainult informatiivsetest positsioonidest koosnevaid järjestusi, märkida mutatsioonide arv igale puuharule, leida kõige tõenäolisem sugupuu .
Vastus:
1)A ACAAACAGTT CGATCGATTT GCAGTCTGGG
2)B ACAAACAGTT TCTAGCGATT GCAGTCAGGG
3)C ACAGACAGTT CGATCGATTT GCAGTCTCGG
4)D ACTGACAGTT CGATCGATTT GCAGTCAGAG
1.
2.
3.
4.
Sama on võimalik ka A ja T puhul.

Võrrelda tulemusi.
Vastus:
Juurteta puu näitab ainult evolutsioonilisi kaugusi, kuid juurtega puu näitab ka põlvnemise ühisest eellasest.

DNA järjestuste fülogeneetiliste puude arvutamine kasutades erinevaid fülogeneetiliste puude koostamise programme .

Leida geeni rrsH (KEGG, iseloomustada lühidalt) järjestused järgmistele organismidele:
Vastus:

Escherichia coli K12 MG1655
http://www.genome.jp/dbget-bin/www_bget?eco:b0201
>eco:b0201 rrsH; 16S ribosomal RNA; K01977 16S ribosomal RNA (N)
aaattgaagagtttgatcatggctcagattgaacgctggcggcaggcctaacacatgcaa
gtcgaacggtaacaggaagaagcttgcttctttgctgacgagtggcggacgggtgagtaa
tgtctgggaaactgcctgatggagggggataactactggaaacggtagctaataccgcat
aacgtcgcaagaccaaagagggggaccttcgggcctcttgccatcggatgtgcccagatg
ggattagctagtaggtggggtaacggctcacctaggcgacgatccctagctggtctgaga
ggatgaccagccacactggaactgagacacggtccagactcctacgggaggcagcagtgg
ggaatattgcacaatgggcgcaagcctgatgcagccatgccgcgtgtatgaagaaggcct
tcgggttgtaaagtactttcagcggggaggaagggagtaaagttaatacctttgctcatt
gacgttacccgcagaagaagcaccggctaactccgtgccagcagccgcggtaatacggag
ggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggtttgttaagtca
gatgtgaaatccccgggctcaacctgggaactgcatctgatactggcaagcttgagtctc
gtagaggggggtagaattccaggtgtagcggtgaaatgcgtagagatctggaggaatacc
ggtggcgaaggcggccccctggacgaagactgacgctcaggtgcgaaagcgtggggagca
aacaggattagataccctggtagtccacgccgtaaacgatgtcgacttggaggttgtgcc
cttgaggcgtggcttccggagctaacgcgttaagtcgaccgcctggggagtacggccgca
aggttaaaactcaaatgaattgacgggggcccgcacaagcggtggagcatgtggtttaat
tcgatgcaacgcgaagaaccttacctggtcttgacatccacagaactttccagagatgga
ttggtgccttcgggaactgtgagacaggtgctgcatggctgtcgtcagctcgtgttgtga
aatgttgggttaagtcccgcaacgagcgcaacccttatcttttgttgccagcggtccggc
cgggaactcaaaggagactgccagtgataaactggaggaaggtggggatgacgtcaagtc
atcatggcccttacgaccagggctacacacgtgctacaatggcgcatacaaagagaagcg
acctcgcgagagcaagcggacctcataaagtgcgtcgtagtccggattggagtctgcaac
tcgactccatgaagtcggaatcgctagtaatcgtggatcagaatgccacggtgaatacgt
tcccgggccttgtacacaccgcccgtcacaccatgggagtgggttgcaaaagaagtaggt
agcttaaccttcgggagggcgcttaccactttgtgattcatgactggggtgaagtcgtaa
caaggtaaccgtaggggaacctgcggttggatcacctcctta

Escherichia coli O157 EDL933
http://www.genome.jp/dbget-bin/www_bget?ece:Z0213
>ece:Z0213 rrsH; 16S ribosomal RNA; K01977 16S ribosomal RNA (N)
aaattgaagagtttgatcatggctcagattgaacgctggcggcaggcctaacacatgcaa
gtcgaacggtaacaggaagaagcttgcttctttgctgacgagtggcggacgggtgagtaa
tgtctgggaaactgcctgatggagagggataactactggaaacggtagctaataccgcat
aacgtcgcaagaccaaagagggggaccttcgggcctcttgccatcggatgtgcccagatg
ggattagctagtaggtggggtaacggctcacctaggcgacgatccctagctggtctgaga
ggatgaccagccacactggaactgagacacggtccagactcctacgggaggcagcagtgg
ggaatattgcacaatgggcgcaagcctgatgcagccatgccgcgtgtatgaagaaggcct
tcgggttgtaaagtactttcagcggggaggaagggagtaaagttaatacctttgctcatt
gacgttacccgcagaagaagcaccggctaactccgtgccagcagccgcggtaatacggag
ggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggtttgttaagtca
gatgtgaaatccccgggctcaacctgggaactgcatctgatactggcaagcttgagtctc
gtagaggggggtagaattccaggtgtagcggtgaaatgcgtagagatctggaggaatacc
ggtggcgaaggcggccccctggacgaagactgacgctcaggtgcgaaagcgtggggagca
aacaggattagataccctggtagtccacgccgtaaacgatgtcgacttggaggttgtgcc
cttgaggcgtggcttccggagctaacgcgttaagtcgaccgcctggggagtacggccgca
aggttaaaactcaaatgaattgacgggggcccgcacaagcggtggagcatgtggtttaat
tcgatgcaacgcgaagaaccttacctggtcttgacatccacagaactttccagagatgga
ttggtgccttcgggaactgtgagacaggtgctgcatggctgtcgtcagctcgtgttgtga
aatgttgggttaagtcccgcaacgagcgcaacccttatcctttgttgccagcggtccggc
cgggaactcaaaggagactgccagtgataaactggaggaaggtggggatgacgtcaagtc
atcatggcccttacgaccagggctacacacgtgctacaatggcgcatacaaagagaagcg
acctcgcgagagcaagcggacctcataaagtgcgtcgtagtccggattggagtctgcaac
tcgactccatgaagtcggaatcgctagtaatcgtggatcagaatgccacggtgaatacgt
tcccgggccttgtacacaccgcccgtcacaccatgggagtgggttgcaaaagaagtaggt
agcttaaccttcgggagggcgcttaccactttgtgattcatgactggggtgaagtcgtaa
caaggtaaccgtaggggaacctgcggttggatcacctcctta

Salmonella typhimurium LT2
http://www.genome.jp/dbget-bin/www_bget?stm:STM0249
>stm:STM0249 rrsH; 16S ribosomal RNA; K01977 16S ribosomal RNA (N)
gtttgatcatggctcagattgaacgctggcggcaggcctaacacatgcaagtcgaacggt
aacaggaagcagcttgctgcttcgctgacgagtggcggacgggtgagtaatgtctgggaa
actgcctgatggagggggataactactggaaacggtggctaataccgcataacgtcgcaa
gaccaaagagggggaccttcgggcctcttgccatcagatgtgcccagatgggattagcta
gttggtgaggtaacggctcaccaaggcgacgatccctagctggtctgagaggatgaccag
ccacactggaactgagacacggtccagactcctacgggaggcagcagtggggaatattgc
acaatgggcgcaagcctgatgcagccatgccgcgtgtatgaagaaggccttcgggttgta
aagtactttcagcggggaggaaggtgttgtggttaataaccgcagcaattgacgttaccc
gcagaagaagcaccggctaactccgtgccagcagccgcggtaatacggagggtgcaagcg
ttaatcggaattactgggcgtaaagcgcacgcaggcggtctgtcaagtcggatgtgaaat
ccccgggctcaacctgggaactgcattcgaaactggcaggcttgagtcttgtagaggggg
gtagaattccaggtgtagcggtgaaatgcgtagagatctggaggaataccggtggcgaag
gcggccccctggacaaagactgacgctcaggtgcgaaagcgtggggagcaaacaggatta
gataccctggtagtccacgccgtaaacgatgtctacttggaggttgtgcccttgaggcgt
ggcttccggagctaacgcgttaagtagaccgcctggggagtacggccgcaaggttaaaac
tcaaatgaattgacgggggcccgcacaagcggtggagcatgtggtttaattcgatgcaac
gcgaagaaccttacctggtcttgacatccacagaactttccagagatggattggtgcctt
cgggaactgtgagacaggtgctgcatggctgtcgtcagctcgtgttgtgaaatgttgggt
taagtcccgcaacgagcgcaacccttatcctttgttgccagcggttaggccgggaactca
aaggagactgccagtgataaactggaggaaggtggggatgacgtcaagtcatcatggccc
ttacgaccagggctacacacgtgctacaatggcgcatacaaagagaagcgacctcgcgag
agcaagcggacctcataaagtgcgtcgtagtccggattggagtctgcaactcgactccat
gaagtcggaatcgctagtaatcgtggatcagaatgccacggtgaatacgttcccgggcct
tgtacacaccgcccgtcacaccatgggagtgggttgcaaaagaagtaggtagcttaacct
tcgggagggcgcttaccactttgtgattcatgactggggtgaagtcgtaacaaggtaacc
gtaggggaacctgcggttggatcacctccttaccttaaagaagc

Shigella flexneri 301
http://www.genome.jp/dbget-bin/www_bget?sfl:SF4435
>sfl:SF4435 rrsH; 16S ribosomal RNA; K01977 16S ribosomal RNA (N)
aaattgaagagtttgatcatggctcagattgaacgctggcggcaggcctaacacatgcaa
gtcgaacggtaacaggaagcgcttgctgcttcgctgacgagtggcggacgggtgagtaat
gtctgggaaactgcctgatggagggggataactactggaaacggtagctaataccgcata
acgtcgcaagaccaaagagggggaccttcgggcctcttgccatcggatgtgcccagatgg
gattagcttgttggtggggtaacggctcaccaaggcgacgatccctagctggtctgagag
gatgaccagccacactggaactgagacacggtccagactcctacgggaggcagcagtggg
gaatattgcacaatgggcgcaagcctgatgcagccatgccgcgtgtatgaagaaggcctt
cgggttgtaaagtactttcagcggggaggaagggagtaaagttaatacctttgctcattg
acgttacccgcagaagaagcaccggctaactccgtgccagcagccgcggtaatacggagg
gtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggtttgttaagtcag
atgtgaaatccccgggctcaacctgggaactgcatctgatactggcaagcttgagtctcg
tagaggggggtagaattccaggtgtagcggtgaaatgcgtagagatctggaggaataccg
gtggcgaaggcgtccccctggacgaagactgacgctcaggtgcgaaagcgtggggagcaa
acaggattagataccctggtagtccacgccgtaaacgatgtcgacttggaggttgtgccc
ttgaggcgtggcttccggagctaacgcgttaagtcgaccgcctggggagtacggccgcaa
ggttaaaactcaaatgaattgacgggggcccgcacaagcggtggagcatgtggtttaatt
cgatgcaacgcgaagaaccttacctggtcttgacatccacggaagttttcagagatgaga
atgtgccttcgggaaccgtgagacaggtgctgcatggctgtcgtcagctcgtgttgtgaa
atgttgggttaagtcccgcaacgagcgcaacccttatcctttgttgccagcggtccggcc
gggaactcaaaggagactgccagtgataaactggaggaaggtggggatgacgtcaagtca
tcatggcccttacgaccagggctacacacgtgctacaatggcgcatacaaagagaagcga
cctcgcgagagcaagcggacctcataaagtgcgtcgtagtccggattggagtctgcaact
cgactccatgaagtcggaatcgctagtaatcgtggatcagaatgccacggtgaatacgtt
cccgggccttgtacacaccgcccgtcacaccatgggagtgggttgcaaaagaagtaggta
gcttaaccttcgggagggcgcttaccactttgtgattcatgactggggtgaagtcgtaac
aaggtaaccgtaggggaacctgcggttggatcacctcctta

Salmonella enterica serovar Paratyphi A
http://www.genome.jp/dbget-bin/www_bget?spt:SPA0256
>spt:SPA0256 rrsH; 16S ribosomal RNA; K01977 16S ribosomal RNA (N)
aattgaagagtttgatcatggctcagattgaacgctggcggcaggcctaacacatgcaag
tcgaacggtaacaggaagcagcttgctgctttgctgacgagtggcggacgggtgagtaat
gtctgggaaactgcctgatggagggggataactactggaaacggtggctaataccgcata
acgtcgcaagaccaaagagggggaccttcgggcctcttgccatcagatgtgcccagatgg
gattagcttgttggtgaggtaacggctcaccaaggcgacgatccctagctggtctgagag
gatgaccagccacactggaactgagacacggtccagactcctacgggaggcagcagtggg
gaatattgcacaatgggcgcaagcctgatgcagccatgccgcgtgtatgaagaaggcctt
cgggttgtaaagtactttcagcggggaggaaggtgttgtggttaataaccgcagcaattg
acgttacccgcagaagaagcaccggctaactccgtgccagcagccgcggtaatacggagg
gtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggtctgtcaagtcgg
atgtgaaatccccgggctcaacctgggaactgcattcgaaactggcaggcttgagtcttg
tagaggggggtagaattccaggtgtagcggtgaaatgcgtagagatctggaggaataccg
gtggcgaaggcggccccctggacaaagactgacgctcaggtgcgaaagcgtggggagcaa
acaggattagataccctggtagtccacgccgtaaacgatgtctacttggaggttgtgccc
ttgaggcgtggcttccggagctaacgcgttaagtagaccgcctggggagtacggccgcaa
ggttaaaactcaaatgaattgacgggggcccgcacaagcggtggagcatgtggtttaatt
cgatgcaacgcgaagaaccttacctggtcttgacatccacggaagttttcagagatgaga
atgtgccttcgggaaccgtgagacaggtgctgcatggctgtcgtcagctcgtgttgtgaa
atgttgggttaagtcccgcaacgagcgcaacccttatcctttgttgccagcggtccggcc
gggaactcaaaggagactgccagtgataaactggaggaaggtggggatgacgtcaagtca
tcatggcccttacgaccagggctacacacgtgctacaatggcgcatacaaagagaagcga
cctcgcgagagcaagcggacctcataaagtgcgtcgtagtccggattggagtctgcaact
cgactccatgaagtcggaatcgctagtaatcgtggatcagaatgccacggtgaatacgtt
cccgggccttgtacacaccgcccgtcacaccatgggagtgggttgcaaaagaagtaggta
gcttaaccttcgggagggcgcttaccactttgtgattcatgactggggtgaagtcgtaac
aaggtaaccgtaggggaacctgcggttggatcacctccttacctta

Sooritada antud järjestuste MSA kasutades mõnda programmi (näiteks ClustalW, EBI).
Vastus:
CLUSTAL W (1.83) multiple sequence alignment
eco_b0201 AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAA 60
ece_Z0213 AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAA 60
sfl_SF4435 AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAA 60
stm_STM0249 ----------GTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAA 50
spt_SPA0256 -AATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAA 59
**************************************************
eco_b0201 GTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAA 120
ece_Z0213 GTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAA 120
sfl_SF4435 GTCGAACGGTAACAGGAAGC-GCTTGCTGCTTCGCTGACGAGTGGCGGACGGGTGAGTAA 119
stm_STM0249 GTCGAACGGTAACAGGAAGCAGCTTGCTGCTTCGCTGACGAGTGGCGGACGGGTGAGTAA 110
spt_SPA0256 GTCGAACGGTAACAGGAAGCAGCTTGCTGCTTTGCTGACGAGTGGCGGACGGGTGAGTAA 119
******************* ******* *** ***************************
eco_b0201 TGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCAT 180
ece_Z0213 TGTCTGGGAAACTGCCTGATGGAGAGGGATAACTACTGGAAACGGTAGCTAATACCGCAT 180
sfl_SF4435 TGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCAT 179
stm_STM0249 TGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTGGCTAATACCGCAT 170
spt_SPA0256 TGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTGGCTAATACCGCAT 179
************************ ********************* *************
eco_b0201 AACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATG 240
ece_Z0213 AACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATG 240
sfl_SF4435 AACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATG 239
stm_STM0249 AACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATG 230
spt_SPA0256 AACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATG 239
********************************************* **************
eco_b0201 GGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGA 300
ece_Z0213 GGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGA 300
sfl_SF4435 GGATTAGCTTGTTGGTGGGGTAACGGCTCACCAAGGCGACGATCCCTAGCTGGTCTGAGA 299
stm_STM0249 GGATTAGCTAGTTGGTGAGGTAACGGCTCACCAAGGCGACGATCCCTAGCTGGTCTGAGA 290
spt_SPA0256 GGATTAGCTTGTTGGTGAGGTAACGGCTCACCAAGGCGACGATCCCTAGCTGGTCTGAGA 299
********* ** **** ************** ***************************
eco_b0201 GGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGG 360
ece_Z0213 GGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGG 360
sfl_SF4435 GGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGG 359
stm_STM0249 GGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGG 350
spt_SPA0256 GGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGG 359
************************************************************
eco_b0201 GGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCT 420
ece_Z0213 GGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCT 420
sfl_SF4435 GGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCT 419
stm_STM0249 GGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCT 410
spt_SPA0256 GGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCT 419
************************************************************
eco_b0201 TCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATT 480
ece_Z0213 TCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATT 480
sfl_SF4435 TCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATT 479
stm_STM0249 TCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGTTGTGGTTAATAACCGCAGCAATT 470
spt_SPA0256 TCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGTTGTGGTTAATAACCGCAGCAATT 479
********************************** * ******* * ***
eco_b0201 GACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAG 540
ece_Z0213 GACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAG 540
sfl_SF4435 GACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAG 539
stm_STM0249 GACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAG 530
spt_SPA0256 GACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAG 539
************************************************************
eco_b0201 GGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCA 600
ece_Z0213 GGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCA 600
sfl_SF4435 GGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCA 599
stm_STM0249 GGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCG 590
spt_SPA0256 GGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCG 599
************************************************* *** *****
eco_b0201 GATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTC 660
ece_Z0213 GATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTC 660
sfl_SF4435 GATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTC 659
stm_STM0249 GATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGGCAGGCTTGAGTCTT 650
spt_SPA0256 GATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGGCAGGCTTGAGTCTT 659
************************************ ** ******* **********
eco_b0201 GTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACC 720
ece_Z0213 GTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACC 720
sfl_SF4435 GTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACC 719
stm_STM0249 GTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACC 710
spt_SPA0256 GTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACC 719
************************************************************
eco_b0201 GGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCA 780
ece_Z0213 GGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCA 780
sfl_SF4435 GGTGGCGAAGGCGTCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCA 779
stm_STM0249 GGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCA 770
spt_SPA0256 GGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCA 779
************* ********** ***********************************
eco_b0201 AACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCC 840
ece_Z0213 AACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCC 840
sfl_SF4435 AACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCC 839
stm_STM0249 AACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCTACTTGGAGGTTGTGCC 830
spt_SPA0256 AACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCTACTTGGAGGTTGTGCC 839
******************************************* ****************
eco_b0201 CTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCA 900
ece_Z0213 CTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCA 900
sfl_SF4435 CTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCA 899
stm_STM0249 CTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTAGACCGCCTGGGGAGTACGGCCGCA 890
spt_SPA0256 CTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTAGACCGCCTGGGGAGTACGGCCGCA 899
*********************************** ************************
eco_b0201 AGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAAT 960
ece_Z0213 AGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAAT 960
sfl_SF4435 AGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAAT 959
stm_STM0249 AGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAAT 950
spt_SPA0256 AGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAAT 959
************************************************************
eco_b0201 TCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGA 1020
ece_Z0213 TCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGA 1020
sfl_SF4435 TCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAG 1019
stm_STM0249 TCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGA 1010
spt_SPA0256 TCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAG 1019
***************************************** *** *** ********
eco_b0201 TTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGA 1080
ece_Z0213 TTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGA 1080
sfl_SF4435 AATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGA 1079
stm_STM0249 TTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGA 1070
spt_SPA0256 AATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGA 1079
************** ******************************************
eco_b0201 AATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCTTTTGTTGCCAGCGGTCCGGC 1140
ece_Z0213 AATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGC 1140
sfl_SF4435 AATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGC 1139
stm_STM0249 AATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTTAGGC 1130
spt_SPA0256 AATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGC 1139
*************************************** *************** ***
eco_b0201 CGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTC 1200
ece_Z0213 CGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTC 1200
sfl_SF4435 CGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTC 1199
stm_STM0249 CGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTC 1190
spt_SPA0256 CGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTC 1199
************************************************************
eco_b0201 ATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCG 1260
ece_Z0213 ATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCG 1260
sfl_SF4435 ATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCG 1259
stm_STM0249 ATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCG 1250
spt_SPA0256 ATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCG 1259
************************************************************
eco_b0201 ACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAAC 1320
ece_Z0213 ACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAAC 1320
sfl_SF4435 ACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAAC 1319
stm_STM0249 ACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAAC 1310
spt_SPA0256 ACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAAC 1319
************************************************************
eco_b0201 TCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGT 1380
ece_Z0213 TCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGT 1380
sfl_SF4435 TCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGT 1379
stm_STM0249 TCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGT 1370
spt_SPA0256 TCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGT 1379
************************************************************
eco_b0201 TCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGT 1440
ece_Z0213 TCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGT 1440
sfl_SF4435 TCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGT 1439
stm_STM0249 TCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGT 1430
spt_SPA0256 TCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGT 1439
************************************************************
eco_b0201 AGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAA 1500
ece_Z0213 AGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAA 1500
sfl_SF4435 AGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAA 1499
stm_STM0249 AGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAA 1490
spt_SPA0256 AGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAA 1499
************************************************************
eco_b0201 CAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA------------ 1542
ece_Z0213 CAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA------------ 1542
sfl_SF4435 CAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA------------ 1541
stm_STM0249 CAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTACCTTAAAGAAGC 1544
spt_SPA0256 CAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTACCTTA------- 1546
******************************************

Moodustada nende järjestuste jaoks fülogeneetilised puud kasutades erinevatel arvutusmeetoditel (kaugusmeetodid, MP, ML) baseeruvaid fülogeneetiliste puude koostamise programme PHYLIP paketis ( http://evolution.genetics.washington.edu/phylip.html , tutvuda programmide dokumentatsiooniga, kasutusjuhend http://koti.mbnet.fi/tuimala/oppaat/phylip2.pdf ) – salvestatud MSA fail peab olema PHYLIP formaadis :

MP metoodi kasutamisel arvutada fülogeneetilised puud kasutades järgmisi programme:
Vastus:

DNAPARS
DNA parsimony algorithm, version 3.66
One most parsimonious tree found :
+spt_SPA025
+--3
+--2 +stm_STM024
| |
| +sfl_SF4435
1-ece_Z0213
+eco_b0201
requires a total of 82.000
between and length
------- --- ------
1 2 0.006113
2 3 0.021879
3 spt_SPA025 0.003539
3 stm_STM024 0.015122
2 sfl_SF4435 0.004826
1 ece_Z0213 0.000644
1 eco_b0201 0.000644

DNAPENNY
Penny algorithm for DNA, version 3.66
branch -and- bound to find all most parsimonious trees
requires a total of 82.000
One most parsimonious tree found:
+-----------eco_b0201
! +--stm_STM024
1 +--3
! +--2 +--spt_SPA025
! ! !
+--4 +-----sfl_SF4435
+--------ece_Z0213
remember: this is an unrooted tree!

DNAMOVE
(spt_SPA025,(stm_STM024,(sfl_SF4435,(ece_Z0213,eco_b0201))));

Joonistada välja juurtega (DRAWGRAM) ja juurteta puu (DRAWTREE). Joonistamisel tuleb valida Bitmapi formaat resolutsiooniga 640 ja 400.
Vastus:
a) DNAPARS
DRAWGRAM:
DRAWTREE:
b) DNAPENNY
DRAWGRAM:
DRAWTREE:
c) DNAMOVE
DRAWGRAM:
DRAWTREE:

Kaugusmeetodite kasutamisel moodustada kõigepealt kaugusmaatriks kasutades DNADIST ning puud arvutada järgmiste programmidega:
Vastus:
Kaugusmaatriks:
5
eco_b0201 0.000000 0.001298 0.011146 0.023964 0.028571
ece_Z0213 0.001298 0.000000 0.011146 0.023963 0.028570
sfl_SF4435 0.011146 0.011146 0.000000 0.027387 0.019786
stm_STM024 0.023964 0.023963 0.027387 0.000000 0.008521
spt_SPA025 0.028571 0.028570 0.019786 0.008521 0.000000

FITCH
DRAWGRAM:
DRAWTREE:

KITSCH
DRAWGRAM:
DRAWTREE:

NEIGHBOR
DRAWGRAM:
DRAWTREE:

Joonistada välja juurtega (DRAWGRAM) ja juurteta puu (DRAWTREE).

ML meetodi kasutamisel teha kõigepealt MSA-le bootstrapping (SEQBOOT) ning seejärel arvutada fülogeneetilised puud kasutades programme (mitte unustada, et meil on multiple datasets – tuleb panna sama number (replicates), mis bootstrapi tegemisel):

DNAML

DNAMLK

Konsensuspuu leidmisel kasutada programmi CONSENSE.
Vastus:
Nucleic acid sequence
Maximum Likelihood method with molecular clock , version 3.66
Empirical Base Frequencies:
A 0.24439
C 0.24556
G 0.30445
T(U) 0.20560
Transition/transversion ratio = 2.000000
+stm_STM024
+--4
! +spt_SPA025
--3
! +sfl_SF4435
+--2
! +ece_Z0213
+--1
+eco_b0201
Ln Likelihood = - 2440 .90431
Ancestor Node Node Height Length
-------- ---- ---- ------ ------
root 3
3 4 0.00784 0.00784
4 stm_STM024 0.01078 0.00294
4 spt_SPA025 0.01078 0.00294
3 2 0.00733 0.00733
2 sfl_SF4435 0.01078 0.00345
2 1 0.00986 0.00253
1 ece_Z0213 0.01078 0.00092
1 eco_b0201 0.01078 0.00092

Analüüsida tulemusi ning võrrelda omavahel lähtudes programmide algoritmidest (juhend!).
Vastus:
Samade meetoditega tulid puud suhteliselt sarnased, kuid eri meetodeid kasutades tulid ka suhteliselt erinevad puud. Näiteks DNADIST, FITCH, KITSCH ja NEIGHBOR võrdlesid järjestusi kaugmaatriksite põhjal. DNAML ja DNAMLK arvestasid iga elemendi asenduse tõenäosusega ning leidsid kõik võimalikud puud.
Distance methods
These programs are intended to be used sequentially. First a distance matrix is calculated by
dnadist or protdist program from the multiple sequence alignment. The matrix is then
transformed into a tree by fitch, kitsch or neighbor program. Programs dnadist and protdist
create a file “outfile”. Before running fitch, kitsch ot neighbor, “outfile” should be renamed,
either as “infile” ot with another file name. Fitch, kitsch and neighbor programs create both
“outfile” and “outtree”.
dnadist -DNA distance matrix calculation
protdist - Protein distance matrix calculation
fitch -Fitch-Margoliash tree drawing method without molecular clock
kitsch -Fitch-Margoliash tree drawing method with molecular clock
neighbor -Neighbor-Joining and UPGMA tree drawing method
Character based methods
These programs read in the sequence alignment, and produce either one or multiple trees in
the output files "outfile" and "outtree".
dnapars -DNA parsimony
dnapenny -DNA parsimony using branch-and-bound
dnaml -DNA maximum likelihood without molecular clock
dnamlk -DNA maximum likelihood with molecular clock
protpars -Protein parsimony
proml -Protein maximum likelihood
Tree drawing
These programs draw a tree from the specifications ("outtree") in the Newick- format . For
example, the specification can be a file produced by the program dnaml. Drawgram and
drawtree produce plotfile, whereas retree saves the result in a file “outtree” (so “outtree” can
not be used as an input to this program).
drawgram -Draws a rooted tree
drawtree -Draws an unrooted tree
retree -Interactive tree-rearrangement
Consensus trees
This program constructs a consensus tree from multiple trees. For example, dnapars can
produce multiple trees, which can be summarized by the program Consense. Also the results
of the bootstrapping are summarized by the program Consense as a majority rule tree.
consense -Draws consensus trees from multiple trees
Tree distances
This program computes, e.g., a topology-based distance between two or more trees. The
distance can be used to assess or compare the results from different analyses.
treedist -Computes distances between trees based on tree topology

.DOC Laadi alla originaalfail 21 lk · .doc · 38 allalaadimist

100 punkti Autor soovib selle materjali allalaadimise eest saada 100 punkti.

~ 21 lehte Lehekülgede arv dokumendis

2012-11-01 Kuupäev, millal dokument üles laeti

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Mumm Õppematerjali autor

Bioinformaatika ülesanded koos lahenduste ja vastustega

Fülogeneetilised puud Bioinformaatika raud matrix formaat kvantitatiivne

Kasutatud allikad

Sarnased õppematerjalid

doc

Bioinformaatika ülesanded II - Fülogeneetilised puud.

olema PHYLIP formaadis: 1. MP metoodi kasutamisel arvutada fülogeneetilised puud kasutades järgmisi programme: a. DNAPARS b. DNAPENNY c. DNAMOVE d. Joonistada välja juurtega (DRAWGRAM) ja juurteta puu (DRAWTREE). Joonistamisel tuleb valida Bitmapi formaat resolutsiooniga 640 ja 400. 2. Kaugusmeetodite kasutamisel moodustada kõigepealt kaugusmaatriks kasutades DNADIST ning puud arvutada järgmiste programmidega: a. FITCH b. KITSCH c. NEIGHBOR d. Joonistada välja juurtega (DRAWGRAM) ja juurteta puu (DRAWTREE). 3. ML meetodi kasutamisel teha kõigepealt MSA-le bootstrapping

Bioinformaatika