Vajad kellegagi rääkida?
Küsi julgelt abi LasteAbi
Logi sisse

Bioinformaatika ülesanded (0)

5 VÄGA HEA
Punktid

Esitatud küsimused

  • Milliste ülesannete lahendamisel on vajalik järjestuste joondamine?
  • Millise nähtusega võiks tegemist olla?

Bioinformaatika ülesanded

Järjestuste paaride joondamine (dot- plot , dünaamiline programmeerimine , skoorid).


  • Milliste ülesannete lahendamisel on vajalik järjestuste joondamine?
  • Kasutada suvalist dot ploti visualiseerimise programmi (näiteks DotMatcher http://mfgn.usm.edu/cgi-bin/emboss.pl?_action=input&_app=dotmatcher või DotPlot’i applet http://arbl.cvmbs.colostate.edu/molkit/dnadot/index.html ). Leida järgnevate nukleotiidsete järjestuste paaride sarnased piirkonnad erinevatel raami suurustel ja sarnasuse piirväärtustel – raam = 1, lim = 0. Leida kõik suuremad sarnased piirkonnad varieerides raami ja piirväärtuse suurust, põhjendada tulemuste seost parameetrite väärtustega. Millise nähtusega võiks tegemist olla?
    • atgttgatgattaaaggaattatttttgatatggacggtgttttatttgatacagaacctttttatctgaggcgacgagaagatttttttaagacaaagggaattcccattgatcacttgaactctaaagattttattgggggcaatctccaagaattatggaaagagttgttaggtaaaaatagggatgatgctatcgttaaggcaattacaactgactatgacgcttacaaacaagcgcataagcctccttatcaaaaactgttgattacagaagtgaactcttgtcttgaacagttgaaaaaacaaggtatcaaactggctgtggcatcaaactcgaagcgtcaggatgttttgttggcgttggagacaacgcaaataaaagattattttgaaataatcctagcgcgtgaagatgtttctagaggcaaaccttatccagatatttataataaagcagtacaaaaactaggattacaaaaaaaacaactgcttgtagtagaagacagccaaaaaggcattgctgccgctaaagcagccaatctgacagtttttgccattaccgactaccgatatggcattgatcagagtcaagctgatcacaagatagatcatttaggacaactgtgtgtaaaaatcggttgttttggatcgtga

    tatcaaaaactgttgattacagaagtgaactcttgtcttgaacagttgaaaaaacaaggtatcaaactggctgtggcatcaaactcgaagcgtcaggatgttttgttggcgttggagacaacgcaaataaaagattattttgaaataatcctagcgcgtgaagatgtttctagaggcaaaccttatccagatatttataataaagcagtacaaaaactaggattacaaaaaaaacaactgcttgtagtagaagacagccaaaaaggcattgctgccgctaaagcagccaatctgacagtttttgccattaccgactaccgatatggcattgatcagagtcaagctgatcacaagatagatcatttaggacaactgtgtgtaaaaatcggttgttttggatcgtgaatgttgatgattaaaggaattatttttgatatggacggtgttttatttgatacagaacctttttatctgaggcgacgagaagatttttttaagacaaagggaattcccattgatcacttgaactctaaagattttattgggggcaatctccaagaattatggaaagagttgttaggtaaaaatagggatgatgctatcgttaaggcaattacaactgactatgacgcttacaaacaagcgcataagcctcct
    Vastus: On näha, et korduvaid järjestusi ei ole. Ühe järjestuse algus on teise lõpp
    • atgttgatgattaaaggaattatttttgatatggacggtgttttatttgatacagaacctttttatctgaggcgacgagaagatttttttaagacaaagggaattcccattgatcacttgaactctaaagattttattgggggcaatctccaagaattatggaaagagttgttaggtaaaaatagggatgatgctatcgttaaggcaattacaactgactatgacgcttacaaacaagcgcataagcctccttatcaaaaactgttgattacagaagtgaactcttgtcttgaacagttgaaaaaacaaggtatcaaactggctgtggcatcaaactcgaagcgtcaggatgttttgttggcgttggagacaacgcaaataaaagattattttgaaataatcctagcgcgtgaagatgtttctagaggcaaaccttatccagatatttataataaagcagtacaaaaactaggattacaaaaaaaacaactgcttgtagtagaagacagccaaaaaggcattgctgccgctaaagcagccaatctgacagtttttgccattaccgactaccgatatggcattgatcagagtcaagctgatcacaagatagatcatttaggacaactgtgtgtaaaaatcggttgttttggatcgtga

    atgttgatgattaaaggaattatttttgatatggacggtgttttatttgatacagaacctttttatctgaggcgacgagaagatttttttaagacaaagggaattcccattgatcacttgaactctaaagattttattgggggcaatctccaagaattatggaaagagttgttaggtaaaaatagggatgatgctatcgttgggcaatctccaagaattatggaaagagttgttaggtaaaaatagggatgatgctatcgttgggcaatctccaagaattatggaaagagttgttaggtaaaaatagggatgatgctatcgttgggcaatctccaagaattatggaaagagttgttaggtaaaaataggggatgttttgttggcgttggagacaacgcaaataaaagattattttgaaataatcctagcgcgtgaagatgtttctagaggcaaaccttatccagatatttataataaagcagtacaaaaactaggattacaaaaaaaacaactgcttgtagtagaagacagccaaaaaggcattgctgccgctaaagcagccaatctgacagtttttgccattaccgactaccgatatggcattgatcagagtcaagctgatcacaagatagatcatttaggacaactgtgtgtaaa
    Vastus: Järjestused on osaliselt sarnased, st esineb identseid lõike.
    • atgttgatgattaaaggaattatttttgatatggacggtgttttatttgatacagaacctttttatctgaggcgacgagaagatttttttaagacaaagggaattcccattgatcacttgaactctaaagattttattgggggcaatctccaagaattatggaaagagttgttaggtaaaaatagggatgatgctatcgttaaggcaattacaactgactatgacgcttacaaacaagcgcataagcctccttatcaaaaactgttgattacagaagtgaactcttgtcttgaacagttgaaaaaacaaggtatcaaactggctgtggcatcaaactcgaagcgtcaggatgttttgttggcgttggagacaacgcaaataaaagattattttgaaataatcctagcgcgtgaagatgtttctagaggcaaaccttatccagatatttataataaagcagtacaaaaactaggattacaaaaaaaacaactgcttgtagtagaagacagccaaaaaggcattgctgccgctaaagcagccaatctgacagtttttgccattaccgactaccgatatggcattgatcagagtcaagctgatcacaagatagatcatttaggacaactgtgtgtaaaaatcggttgttttggatcgtga

    atgttgatgatttgaactctaaagattttattcgtagcgatcgtagcgatcgatcgcgccagttgttaggtaaaaatagggatgatgctatcgttaaggcaattacaactgactatgacgcttacaaacaagcgcataagcctccttatcaaaaactgttgattacagaagtgaactcttgtcttgaacagttgaggaattatttttgatatggaaaaaaacaaggtatcaaactggctgtggcatcaaactcgaagcgtcaggatgttttgttggcgttggagacaacgcaaataaaagattattttgaaataatccaggcaaaccttatccagatatttataataaagcagtacaaaaactaggattacaaaaaaaacaactgcttgtagtagaagacagccaaaaaggcattgctgccgctaaagcagccaatctgacagtttttgccattaccgactataacggtgttttatttgatacagaacctttttatctgaggcgacgagaagatttttttaagacaaagggaattcccattgatcacccgatatggcattgatcagagtcaagctgatcacaagatagatcatttaggacaactgtgtgtaaaaatcggttgttttggatcgtgacgatcgatgctagctgatcgat
    Vastus: Peadiagonaal on nihutatud. Järjestused on paralleelsed.
    • atgttgatgattaaaggaattatttttgatatggacggtgttttatttgatacagaacctttttatctgaggcgacgagaagatttttttaagacaaagggaattcccattgatcacttgaactctaaagattttattgggggcaatctccaagaattatggaaagagttgttaggtaaaaatagggatgatgctatcgttaaggcaattacaactgactatgacgcttacaaacaagcgcataagcctccttatcaaaaactgttgattacagaagtgaactcttgtcttgaacagttgaaaaaacaaggtatcaaactggctgtggcatcaaactcgaagcgtcaggatgttttgttggcgttggagacaacgcaaataaaagattattttgaaataatcctagcgcgtgaagatgtttctagaggcaaaccttatccagatatttataataaagcagtacaaaaactaggattacaaaaaaaacaactgcttgtagtagaagacagccaaaaaggcattgctgccgctaaagcagccaatctgacagtttttgccattaccgactaccgatatggcattgatcagagtcaagctgatcacaagatagatcatttaggacaactgtgtgtaaaaatcggttgttttggatcgtga

    atgttgatgcctttttatctgaggcgacgagaagatttttttaagacaaagggaattcccattgatcacttgaatgaaaaaacaaggtatcaaactggctgtggcaatctccaagaattatggaaagagttgttaggtaaaaatagggatgatgctatcgttaaggcaattacaactgactatgacgcttacaaacaagcgcataagccctctaaagattttattgggacagttcctttacagaagtgaactcttgtcttgaggcatcaaactcgaagcgtcaggatgttttgttggcgttggagacaacgcaaataaaagattattttgtattaaaggaattatttttgatatggacggtgttttatttgatacagaaacaaaaaaaacaactgcttgtagtagaagacagccaaaaaggcattgctgccgctaaagcagctatcaaaaactgttgacaatctgacaaataatcctagcgcgtgaagatgtttctagaggcaaaccttatccagatatttataataaagcagtacaaaaactaggatagtttttgccattaccgactaccgatatggcattgatcagagtcaagctgatcacaagatagatcatttaggacaactgtgtgtaaaaatcggttgttttggatcgtga
    Vastus : Peadiagonaal puudub. Tegemist on keerulisema mutatsiooniga, transpositsiooniga.
  • Leida, milline joondamiste paar on sarnasem. Kuidas diferentseerida tühiku trahvi . Kokkulangevus = +1, mittekokkulangevus = -1.
    1.AGATAGAAACTGATATATA 2.AGATAGAAACTGATATATA
    AGA-A-A-ACAGAG-T--- AGA--GA-AGTGAG-T---
    Oletame, et 1 tühiku trahv on -1 ja tühikute seeria pikkuse trahv on -2
    Siis:
    (kokkulangevus) (mittekokkulangevus) (tühik) (seeria pikkus)
    S1= 10 *1 + 2* (-1) + 7*(-1) + 5*(-2) = -9
    (kokkulangevus) (mittekokkulangevus) (tühik) (seeria pikkus)
    S2= 10*1 + 2* (-1) + 7*(-1) + 4*(-2) = -7
  • Konstrueerida oma skoorimaatriks järgmistele aminohapetele nende füüsikaliste omaduste põhjal. Lisada põhjendused.
  • Ala, Gly, Cys, Trp, Lys, Ile.
    Ala(A)
    Gly(G)
    Cys(C)
    Trp(W)
    Lys(K)
    Ile(I)
    Ala(A)
    0
    Gly(G)
    -1
    0
    Cys(C)
    -1
    -1
    0
    Trp(W)
    -4
    -4
    -3
    0
    Lys(K)
    -5
    -3
    -4
    -3
    0
    Ile(I)
    -3
    -3
    -4
    -3
    -4
    0
    Selgitus :
    Ala on 0.
    Tuleb lugeda, mitu ringi on vaja läbida mingisuguse teise aminohappeni jõudmiseks.
    Ala tuleb lahutada ringist kõik ülejäänud ringid , mida on vaja läbida
  • Leidke käsitsi kahe järjestuse optimaalne globaalne joondamine Needleman-Wunschi algoritmi järgi – kokkulangevus = +1, mittekokkulangevus = 0, tühik = -1.
    ACAGTCGAACG
    ACCGTCCG
    Vastus:
    M=11
    N=8
    A
    C
    A
    G
    T
    C
    G
    A
    A
    C
    G
    0
    -1
    -2
    -3
    -4
    -5
    -6
    -7
    -8
    -9
    -10
    -11
    A
    -1
    1
    0
    -1
    -2
    -3
    -4
    -5
    -6
    -7
    -8
    -9
    C
    -2
    0
    2
    1
    0
    -1
    -2
    -3
    -4
    -5
    -6
    -7
    C
    -3
    -1
    1
    2
    1
    0
    0
    -1
    -2
    -3
    -4
    -5
    G
    -4
    -2
    0
    1
    3
    2
    1
    1
    0
    -1
    -2
    -3
    T
    -5
    -3
    -1
    0
    2
    4
    3
    2
    1
    0
    -1
    -2
    C
    -6
    -4
    -2
    -1
    1
    3
    5
    4
    3
    2
    1
    0
    C
    -7
    -5
    -3
    -2
    0
    2
    4
    5
    4
    3
    3
    2
    G
    -8
    -6
    -4
    -3
    -1
    1
    3
    5
    5
    4
    3
    4
    Maksimumskoor on 5
    A C A G T C G A A C G
    | | | | | | |
    A C C G T C _ _ _ C G
  • Leidke käsitsi kahe järjestuse lokaalne joondamine Smith-Watermani algoritmi järgi – kokkulangevus = +1, mittekokkulangevus = -1, tühik = -1.
    ACGTGACAT
    CGTGAT
    Vastus:
    A C G T G A C A T
    _ C G T G A _ _ _
    A
    C
    G
    T
    G
    A
    C
    A
    T
    0
    0
    0
    0
    0
    0
    0
    0
    0
    0
    C
    0
    0
    1
    0
    0
    0
    0
    0
    0
    0
    G
    0
    0
    0
    2
    1
    1
    0
    0
    0
    0
    T
    0
    0
    0
    1
    3
    2
    1
    0
    0
    0
    G
    0
    0
    0
    1
    2
    4
    3
    2
    1
    0
    A
    0
    1
    0
    0
    1
    3
    5
    4
    3
    2
    T
    0
    0
    0
    0
    1
    2
    4
    4
    3
    4
    Maksimumskoor on 4
    CG T G A
    | | | | |
    C G T G A
  • Sooritada punktis 2 toodud järjestustega paarikaupa globaalne joondamine kasutades vastavat programmi (näiteks EMBOSS’i Align EBI kodulehel http://www.ebi.ac.uk/emboss/align/ ). Varieerida skoorimaatrikseid ja tühikutrahve ning põhjendada erinevusi, võrrelda dot-ploti tulemustega, millise nähtusega on tegemist? Kontrollida punktis 5 tehtud tööd.
    Vastus:
    2. punkti esimese järjestuste paari globaalne joondamine:
    ########################################
    # Program : needle
    # Rundate: Wed Mar 07 18:02:24 2007
    # Align_format: srspair
    # Report_file: /ebi/extserv/old- work /needle-20070307-18022349260605.output
    ########################################
    #=======================================
    # Aligned_sequences: 2
    # 1: EMBOSS_001
    # 2: EMBOSS_001
    # Matrix : EDNAFULL
    # Gap_penalty: 10.0
    # Extend_penalty: 0.5
    # Length: 909
    # Identity : 405/909 (44.6%)
    # Similarity: 405/909 (44.6%)
    # Gaps: 504/909 (55.4%)
    # Score : 2025.0
    #=======================================
    EMBOSS_001 1 atgttgatgattaaaggaattatttttgatatggacggtgttttatttga 50
    EMBOSS_001 1 0
    EMBOSS_001 51 tacagaacctttttatctgaggcgacgagaagatttttttaagacaaagg 100
    EMBOSS_001 1 0
    EMBOSS_001 101 gaattcccattgatcacttgaactctaaagattttattgggggcaatctc 150
    EMBOSS_001 1 0
    EMBOSS_001 151 caagaattatggaaagagttgttaggtaaaaatagggatgatgctatcgt 200
    EMBOSS_001 1 0
    EMBOSS_001 201 taaggcaattacaactgactatgacgcttacaaacaagcgcataagcctc 250
    EMBOSS_001 1 0
    EMBOSS_001 251 cttatcaaaaactgttgattacagaagtgaactcttgtcttgaacagttg 300
    ||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 1 tatcaaaaactgttgattacagaagtgaactcttgtcttgaacagttg 48
    EMBOSS_001 301 aaaaaacaaggtatcaaactggctgtggcatcaaactcgaagcgtcagga 350
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 49 aaaaaacaaggtatcaaactggctgtggcatcaaactcgaagcgtcagga 98
    EMBOSS_001 351 tgttttgttggcgttggagacaacgcaaataaaagattattttgaaataa 400
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 99 tgttttgttggcgttggagacaacgcaaataaaagattattttgaaataa 148
    EMBOSS_001 401 tcctagcgcgtgaagatgtttctagaggcaaaccttatccagatatttat 450
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 149 tcctagcgcgtgaagatgtttctagaggcaaaccttatccagatatttat 198
    EMBOSS_001 451 aataaagcagtacaaaaactaggattacaaaaaaaacaactgcttgtagt 500
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 199 aataaagcagtacaaaaactaggattacaaaaaaaacaactgcttgtagt 248
    EMBOSS_001 501 agaagacagccaaaaaggcattgctgccgctaaagcagccaatctgacag 550
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 249 agaagacagccaaaaaggcattgctgccgctaaagcagccaatctgacag 298
    EMBOSS_001 551 tttttgccattaccgactaccgatatggcattgatcagagtcaagctgat 600
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 299 tttttgccattaccgactaccgatatggcattgatcagagtcaagctgat 348
    EMBOSS_001 601 cacaagatagatcatttaggacaactgtgtgtaaaaatcggttgttttgg 650
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 349 cacaagatagatcatttaggacaactgtgtgtaaaaatcggttgttttgg 398
    EMBOSS_001 651 atcgtga 657
    |||||||
    EMBOSS_001 399 atcgtgaatgttgatgattaaaggaattatttttgatatggacggtgttt 448
    EMBOSS_001 658 657
    EMBOSS_001 449 tatttgatacagaacctttttatctgaggcgacgagaagatttttttaag 498
    EMBOSS_001 658 657
    EMBOSS_001 499 acaaagggaattcccattgatcacttgaactctaaagattttattggggg 548
    EMBOSS_001 658 657
    EMBOSS_001 549 caatctccaagaattatggaaagagttgttaggtaaaaatagggatgatg 598
    EMBOSS_001 658 657
    EMBOSS_001 599 ctatcgttaaggcaattacaactgactatgacgcttacaaacaagcgcat 648
    EMBOSS_001 658 657
    EMBOSS_001 649 aagcctcct 657
    #---------------------------------------
    #---------------------------------------
    EMBOSSi tulemus on DotPloti tulemusest mõnevõrra erinev, kuigi ma ei varieerinud skoorimaatrikseid ja tühikutrahve. DotPlot näitab erinevaid variante , kuid EMBOSS näitab ainult kõige optimaalsemat varianti. EMBOSS näitab kokkulangevust piirkonnas esimese järjestuse 251. nukleotiidist ja teise järjestuse 1. nukleotiidist.
    2. punkti teise järjestuste paari globaalne joondamine:
    ########################################
    # Program: needle
    # Rundate: Wed Mar 07 18:05:51 2007
    # Align_format: srspair
    # Report_file: /ebi/extserv/old-work/needle-20070307-18055071012377.output
    ########################################
    #=======================================
    # Aligned_sequences: 2
    # 1: EMBOSS_001
    # 2: EMBOSS_001
    # Matrix: EBLOSUM62
    # Gap_penalty: 10.0
    # Extend_penalty: 0.5
    # Length: 696
    # Identity: 566/696 (81.3%)
    # Similarity: 566/696 (81.3%)
    # Gaps: 78/696 (11.2%)
    # Score: 2913.5
    #=======================================
    EMBOSS_001 1 atgttgatgattaaaggaattatttttgatatggacggtgttttatttga 50
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 1 atgttgatgattaaaggaattatttttgatatggacggtgttttatttga 50
    EMBOSS_001 51 tacagaacctttttatctgaggcgacgagaagatttttttaagacaaagg 100
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 51 tacagaacctttttatctgaggcgacgagaagatttttttaagacaaagg 100
    EMBOSS_001 101 gaattcccattgatcacttgaactctaaagattttattgggggcaatctc 150
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 101 gaattcccattgatcacttgaactctaaagattttattgggggcaatctc 150
    EMBOSS_001 151 caagaattatggaaagagttgttaggtaaaaatagggatgatgctatcgt 200
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 151 caagaattatggaaagagttgttaggtaaaaatagggatgatgctatcgt 200
    EMBOSS_001 201 taaggcaattacaactgactatg--acgc----tta---caaacaagcgc 241
    | .||||||..|.|...|.|||| |.|. ||| .|||..||.|.
    EMBOSS_001 201 t-gggcaatctccaagaattatggaaagagttgttaggtaaaaataggga 249
    EMBOSS_001 242 ataagc-ctcctt-atcaaaaactgttgattacag-aagtgaactcttgt 288
    ..|.|| .||.|| ..|||...|.....||||..| |||.| ||||
    EMBOSS_001 250 tgatgctatcgttgggcaatctccaagaattatggaaagag-----ttgt 294
    EMBOSS_001 289 cttgaacagttgaaaaaacaaggtatcaaactggctgtggcatcaaactc 338
    |.|..||||..|||.||.|..||..|..||| .|||.|||
    EMBOSS_001 295 ---------taggtaaaaatagggatgatgctatcgttgg--gcaatctc 333
    EMBOSS_001 339 gaagcgtca---------------------------ggatgttttgttgg 361
    .|||..|.| ||||||||||||||
    EMBOSS_001 334 caagaattatggaaagagttgttaggtaaaaataggggatgttttgttgg 383
    EMBOSS_001 362 cgttggagacaacgcaaataaaagattattttgaaataatcctagcgcgt 411
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 384 cgttggagacaacgcaaataaaagattattttgaaataatcctagcgcgt 433
    EMBOSS_001 412 gaagatgtttctagaggcaaaccttatccagatatttataataaagcagt 461
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 434 gaagatgtttctagaggcaaaccttatccagatatttataataaagcagt 483
    EMBOSS_001 462 acaaaaactaggattacaaaaaaaacaactgcttgtagtagaagacagcc 511
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 484 acaaaaactaggattacaaaaaaaacaactgcttgtagtagaagacagcc 533
    EMBOSS_001 512 aaaaaggcattgctgccgctaaagcagccaatctgacagtttttgccatt 561
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 534 aaaaaggcattgctgccgctaaagcagccaatctgacagtttttgccatt 583
    EMBOSS_001 562 accgactaccgatatggcattgatcagagtcaagctgatcacaagataga 611
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 584 accgactaccgatatggcattgatcagagtcaagctgatcacaagataga 633
    EMBOSS_001 612 tcatttaggacaactgtgtgtaaaaatcggttgttttggatcgtga 657
    ||||||||||||||||||||||||
    EMBOSS_001 634 tcatttaggacaactgtgtgtaaa 657
    #---------------------------------------
    #---------------------------------------
    Nii EMBOSS kui ka DotPlot näitavad, et keskel (201-347 nukleotiidi) esineb mittevastavus. DotPlotis näen ka osaliselt korduvaid järjestusi.
    2. punkti kolmanda järjestuste paari globaalne joondamine:
    ########################################
    # Program: needle
    # Rundate: Wed Mar 07 18:08:42 2007
    # Align_format: srspair
    # Report_file: /ebi/extserv/old-work/needle-20070307-18084190762120.output
    ########################################
    #=======================================
    # Aligned_sequences: 2
    # 1: EMBOSS_001
    # 2: EMBOSS_001
    # Matrix: EDNAFULL
    # Gap_penalty: 10.0
    # Extend_penalty: 0.5
    # Length: 793
    # Identity: 509/793 (64.2%)
    # Similarity: 509/793 (64.2%)
    # Gaps: 272/793 (34.3%)
    # Score: 2366.0
    #=======================================
    EMBOSS_001 1 atgttgatgattaaaggaattatttttgatatggacggtgttttatttga 50
    EMBOSS_001 1 0
    EMBOSS_001 51 tacagaacctttttatctgaggcgacgagaagatttttttaagacaaagg 100
    EMBOSS_001 1 0
    EMBOSS_001 101 gaattcccattgatcacttgaactctaaagattttattgggggcaatctc 150
    || .|||||.|.|||||||||||||||||||||.|..||.|||
    EMBOSS_001 1 at----gttgatgatttgaactctaaagattttattcgtagcgatc-- 42
    EMBOSS_001 151 caagaattatggaaag--------agttgttaggtaaaaatagggatgat 192
    .||..||..| ||||||||||||||||||||||||||
    EMBOSS_001 43 ------gtagcgatcgatcgcgccagttgttaggtaaaaatagggatgat 86
    EMBOSS_001 193 gctatcgttaaggcaattacaactgactatgacgcttacaaacaagcgca 242
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 87 gctatcgttaaggcaattacaactgactatgacgcttacaaacaagcgca 136
    EMBOSS_001 243 taagcctccttatcaaaaactgttgattacagaagtgaactcttgtcttg 292
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 137 taagcctccttatcaaaaactgttgattacagaagtgaactcttgtcttg 186
    EMBOSS_001 293 aacagttg---------------------aaaaaacaaggtatcaaactg 321
    |||||||| |||||||||||||||||||||
    EMBOSS_001 187 aacagttgaggaattatttttgatatggaaaaaaacaaggtatcaaactg 236
    EMBOSS_001 322 gctgtggcatcaaactcgaagcgtcaggatgttttgttggcgttggagac 371
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 237 gctgtggcatcaaactcgaagcgtcaggatgttttgttggcgttggagac 286
    EMBOSS_001 372 aacgcaaataaaagattattttgaaataatcctagcgcgtgaagatgttt 421
    ||||||||||||||||||||||||||||||||
    EMBOSS_001 287 aacgcaaataaaagattattttgaaataatcc------------------ 318
    EMBOSS_001 422 ctagaggcaaaccttatccagatatttataataaagcagtacaaaaacta 471
    ||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 319 ----aggcaaaccttatccagatatttataataaagcagtacaaaaacta 364
    EMBOSS_001 472 ggattacaaaaaaaacaactgcttgtagtagaagacagccaaaaaggcat 521
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 365 ggattacaaaaaaaacaactgcttgtagtagaagacagccaaaaaggcat 414
    EMBOSS_001 522 tgctgccgctaaagcagccaatctgacagtttttgccattaccgacta-- 569
    ||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 415 tgctgccgctaaagcagccaatctgacagtttttgccattaccgactata 464
    EMBOSS_001 570 -------------------------------------------------- 569
    EMBOSS_001 465 acggtgttttatttgatacagaacctttttatctgaggcgacgagaagat 514
    EMBOSS_001 570 ---------------------------------ccgatatggcattgatc 586
    |||||||||||||||||
    EMBOSS_001 515 ttttttaagacaaagggaattcccattgatcacccgatatggcattgatc 564
    EMBOSS_001 587 agagtcaagctgatcacaagatagatcatttaggacaactgtgtgtaaaa 636
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 565 agagtcaagctgatcacaagatagatcatttaggacaactgtgtgtaaaa 614
    EMBOSS_001 637 atcggttgttttggatcgtga 657
    |||||||||||||||||||||
    EMBOSS_001 615 atcggttgttttggatcgtgacgatcgatgctagctgatcgat 657
    #---------------------------------------
    #---------------------------------------
    Järjestuste identsus on 64,2%. Ka DotPlot näitab madalat identsust. Esineb mittevastavusi.
    2. punkti neljanda järjestuste paari globaalne joondamine:
    ########################################
    # Program: needle
    # Rundate: Wed Mar 07 18:12:05 2007
    # Align_format: srspair
    # Report_file: /ebi/extserv/old-work/needle-20070307-18120462654439.output
    ########################################
    #=======================================
    # Aligned_sequences: 2
    # 1: EMBOSS_001
    # 2: EMBOSS_001
    # Matrix: EDNAFULL
    # Gap_penalty: 10.0
    # Extend_penalty: 0.5
    # Length: 788
    # Identity: 507/788 (64.3%)
    # Similarity: 507/788 (64.3%)
    # Gaps: 262/788 (33.2%)
    # Score: 2157.0
    #=======================================
    EMBOSS_001 1 atgttgatgattaaaggaattatttttgatatggacggtgttttatttga 50
    |||||||||
    EMBOSS_001 1 atgttgatg----------------------------------------- 9
    EMBOSS_001 51 tacagaacctttttatctgaggcgacgagaagatttttttaagacaaagg 100
    |||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 10 -------cctttttatctgaggcgacgagaagatttttttaagacaaagg 52
    EMBOSS_001 101 gaattcccattgatcacttgaactct----aaagattttat-----tg-- 139
    |||||||||||||||||||||| | |||.|...||| ||
    EMBOSS_001 53 gaattcccattgatcacttgaa---tgaaaaaacaaggtatcaaactggc 99
    EMBOSS_001 140 -ggggcaatctccaagaattatggaaagagttgttaggtaaaaataggga 188
    |.|||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 100 tgtggcaatctccaagaattatggaaagagttgttaggtaaaaataggga 149
    EMBOSS_001 189 tgatgctatcgttaaggcaattacaactgactatgacgcttacaaacaag 238
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 150 tgatgctatcgttaaggcaattacaactgactatgacgcttacaaacaag 199
    EMBOSS_001 239 cgcataagcctccttatcaaaa------------actgtt-gattacaga 275
    |||||||||| .||.||| ||.||| ..|||||||
    EMBOSS_001 200 cgcataagcc----ctctaaagattttattgggacagttcctttacaga 244
    EMBOSS_001 276 agtgaactcttgtcttgaacagttgaaaaaacaaggtatcaaactggctg 325
    ||||||||||||||||||
    EMBOSS_001 245 agtgaactcttgtcttga-------------------------------- 262
    EMBOSS_001 326 tggcatcaaactcgaagcgtcaggatgttttgttggcgttggagacaacg 375
    |||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 263 -ggcatcaaactcgaagcgtcaggatgttttgttggcgttggagacaacg 311
    EMBOSS_001 376 caaataaaagattattttgaaataatcctagcgcgtgaa-gatgtttcta 424
    |||||||||||||||||||.|.||| || ||| .||.|||
    EMBOSS_001 312 caaataaaagattattttgtattaa----ag-----gaattattttt--- 349
    EMBOSS_001 425 gaggcaaaccttatccagatat--------ttataataaagcagtacaaa 466
    ||||| ||.||.|..| ||||.|
    EMBOSS_001 350 -----------------gatatggacggtgttttatttga----tacaga 378
    EMBOSS_001 467 aactaggattacaaaaaaaacaactgcttgtagtagaagacagccaaaaa 516
    | ||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 379 a---------acaaaaaaaacaactgcttgtagtagaagacagccaaaaa 419
    EMBOSS_001 517 ggcattgctgccgctaaagcagc----------------caatctgac-- 548
    ||||||||||||||||||||||| |||||||||
    EMBOSS_001 420 ggcattgctgccgctaaagcagctatcaaaaactgttgacaatctgacaa 469
    EMBOSS_001 549 -------------------------------------------------- 548
    EMBOSS_001 470 ataatcctagcgcgtgaagatgtttctagaggcaaaccttatccagatat 519
    EMBOSS_001 549 -----------------------------agtttttgccattaccgacta 569
    |||||||||||||||||||||
    EMBOSS_001 520 ttataataaagcagtacaaaaactaggatagtttttgccattaccgacta 569
    EMBOSS_001 570 ccgatatggcattgatcagagtcaagctgatcacaagatagatcatttag 619
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 570 ccgatatggcattgatcagagtcaagctgatcacaagatagatcatttag 619
    EMBOSS_001 620 gacaactgtgtgtaaaaatcggttgttttggatcgtga 657
    ||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 620 gacaactgtgtgtaaaaatcggttgttttggatcgtga 657
    #---------------------------------------
    #---------------------------------------
    Nii EMBOSS kui ka DotPlot näitavad järjestuste madalat identsust. Kokkulangevus esineb vaid järjestuste lõpus. DotPloti pilt on suhteliselt segane, sellest on raske midagi järeldada.
    5.punkti kontroll:
    ########################################
    # Program: needle
    # Rundate: Tue Mar 06 06:44:20 2007
    # Align_format: srspair
    # Report_file: /ebi/extserv/old-work/needle-20070306-06442094948578.output
    ########################################
    #=======================================
    # Aligned_sequences: 2
    # 1: EMBOSS_001
    # 2: EMBOSS_001
    # Matrix: EBLOSUM62
    # Gap_penalty: 10.0
    # Extend_penalty: 0.5
    # Length: 11
    # Identity: 7/11 (63.6%)
    # Similarity: 7/11 (63.6%)
    # Gaps: 3/11 (27.3%)
    # Score: 37.0
    #=======================================
    EMBOSS_001 1 ACAGTCGAACG 11
    ||.||| ||
    EMBOSS_001 1 ACCGTC---CG 8
    #---------------------------------------
    ---------------------------------------
    Järeldus: 5. punktis tehtud töö on õige, kuna sain samade parameetritega sama vastuse.
    8.Sooritada punktis 2 toodud järjestustega paarikaupa lokaalne joondamine kasutades vastavat programmi (näiteks EMBOSS’i Align EBI kodulehel http://www.ebi.ac.uk/emboss/align/ ). Varieerida skoorimaatrikseid ja tühikutrahve ning põhjendada erinevusi, kontrollida punktis 6 tehtud tööd.
    Vastus:
    Kuna nii globaalse kui lokaalse joondamise puhul olid teised parameetrid samad, siis EMBOSSiga saadud globaalse joondamise ja lokaalse joondamise tulemused on suhteliselt sarnased.
    2. punkti esimese järjestuste paari lokaalne joondamine:
    ########################################
    # Program: water
    # Rundate: Wed Mar 07 18:16:26 2007
    # Align_format: srspair
    # Report_file: /ebi/extserv/old-work/water-20070307-18162542106346.output
    ########################################
    #=======================================
    # Aligned_sequences: 2
    # 1: EMBOSS_001
    # 2: EMBOSS_001
    # Matrix: EDNAFULL
    # Gap_penalty: 10.0
    # Extend_penalty: 0.5
    # Length: 405
    # Identity: 405/405 (100.0%)
    # Similarity: 405/405 (100.0%)
    # Gaps: 0/405 ( 0.0%)
    # Score: 2025.0
    #=======================================
    EMBOSS_001 253 tatcaaaaactgttgattacagaagtgaactcttgtcttgaacagttgaa 302
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 1 tatcaaaaactgttgattacagaagtgaactcttgtcttgaacagttgaa 50
    EMBOSS_001 303 aaaacaaggtatcaaactggctgtggcatcaaactcgaagcgtcaggatg 352
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 51 aaaacaaggtatcaaactggctgtggcatcaaactcgaagcgtcaggatg 100
    EMBOSS_001 353 ttttgttggcgttggagacaacgcaaataaaagattattttgaaataatc 402
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 101 ttttgttggcgttggagacaacgcaaataaaagattattttgaaataatc 150
    EMBOSS_001 403 ctagcgcgtgaagatgtttctagaggcaaaccttatccagatatttataa 452
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 151 ctagcgcgtgaagatgtttctagaggcaaaccttatccagatatttataa 200
    EMBOSS_001 453 taaagcagtacaaaaactaggattacaaaaaaaacaactgcttgtagtag 502
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 201 taaagcagtacaaaaactaggattacaaaaaaaacaactgcttgtagtag 250
    EMBOSS_001 503 aagacagccaaaaaggcattgctgccgctaaagcagccaatctgacagtt 552
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 251 aagacagccaaaaaggcattgctgccgctaaagcagccaatctgacagtt 300
    EMBOSS_001 553 tttgccattaccgactaccgatatggcattgatcagagtcaagctgatca 602
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 301 tttgccattaccgactaccgatatggcattgatcagagtcaagctgatca 350
    EMBOSS_001 603 caagatagatcatttaggacaactgtgtgtaaaaatcggttgttttggat 652
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 351 caagatagatcatttaggacaactgtgtgtaaaaatcggttgttttggat 400
    EMBOSS_001 653 cgtga 657
    |||||
    EMBOSS_001 401 cgtga 405
    #---------------------------------------
    #---------------------------------------
    Nii nagu ka DotPlot, näitab EMBOSS järjestuste kokkulangevust. EMBOSSi puhul näen, et see on 100%.
    2. punkti teise järjestuste paari lokaalne joondamine:
    ########################################
    # Program: water
    # Rundate: Wed Mar 07 18:19:37 2007
    # Align_format: srspair
    # Report_file: /ebi/extserv/old-work/water-20070307-18193669422759.output
    ########################################
    #=======================================
    # Aligned_sequences: 2
    # 1: EMBOSS_001
    # 2: EMBOSS_001
    # Matrix: EDNAFULL
    # Gap_penalty: 10.0
    # Extend_penalty: 0.5
    # Length: 692
    # Identity: 572/692 (82.7%)
    # Similarity: 572/692 (82.7%)
    # Gaps: 92/692 (13.3%)
    # Score: 2531.0
    #=======================================
    EMBOSS_001 1 atgttgatgattaaaggaattatttttgatatggacggtgttttatttga 50
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 1 atgttgatgattaaaggaattatttttgatatggacggtgttttatttga 50
    EMBOSS_001 51 tacagaacctttttatctgaggcgacgagaagatttttttaagacaaagg 100
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 51 tacagaacctttttatctgaggcgacgagaagatttttttaagacaaagg 100
    EMBOSS_001 101 gaattcccattgatcacttgaactctaaagattttattgggggcaatctc 150
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 101 gaattcccattgatcacttgaactctaaagattttattgggggcaatctc 150
    EMBOSS_001 151 caagaattatggaaagagttgttaggtaaaaatagggatgatgctatcgt 200
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 151 caagaattatggaaagagttgttaggtaaaaatagggatgatgctatcgt 200
    EMBOSS_001 201 taaggcaat-tacaactg-actatg------------acgcttacaaaca 236
    | .|||||| |.||| | |.|||| |.| ||.|||.|
    EMBOSS_001 201 t-gggcaatctccaa--gaattatggaaagagttgttagg--taaaaata 245
    EMBOSS_001 237 agcgcat-aagcctccttatcaaaaactgttg---- attac --agaagt- 278
    .|.|| |.|| |||| |||| ||..| ||||.|
    EMBOSS_001 246 --gggatgatgc-----tatc-------gttgggcaatctccaagaatta 281
    EMBOSS_001 279 --gaactcttgtcttgaacagttg------aaaaaacaaggtatcaaact 320
    || ||.||||| ||||| .|||.||.|..||
    EMBOSS_001 282 tgga------------aagagttgttaggtaaaaa--tagggatgatgct 317
    EMBOSS_001 321 ggctgtggcatcaaactcgaagcgtca----------------------- 347
    ..|..||| .|||.|||.|||..|.|
    EMBOSS_001 318 atcgttgg--gcaatctccaagaattatggaaagagttgttaggtaaaaa 365
    EMBOSS_001 348 ----ggatgttttgttggcgttggagacaacgcaaataaaagattatttt 393
    ||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 366 taggggatgttttgttggcgttggagacaacgcaaataaaagattatttt 415
    EMBOSS_001 394 gaaataatcctagcgcgtgaagatgtttctagaggcaaaccttatccaga 443
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 416 gaaataatcctagcgcgtgaagatgtttctagaggcaaaccttatccaga 465
    EMBOSS_001 444 tatttataataaagcagtacaaaaactaggattacaaaaaaaacaactgc 493
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 466 tatttataataaagcagtacaaaaactaggattacaaaaaaaacaactgc 515
    EMBOSS_001 494 ttgtagtagaagacagccaaaaaggcattgctgccgctaaagcagccaat 543
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 516 ttgtagtagaagacagccaaaaaggcattgctgccgctaaagcagccaat 565
    EMBOSS_001 544 ctgacagtttttgccattaccgactaccgatatggcattgatcagagtca 593
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 566 ctgacagtttttgccattaccgactaccgatatggcattgatcagagtca 615
    EMBOSS_001 594 agctgatcacaagatagatcatttaggacaactgtgtgtaaa 635
    ||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 616 agctgatcacaagatagatcatttaggacaactgtgtgtaaa 657
    #---------------------------------------
    #---------------------------------------
    Lokaalsel joondamisel näen, et järjestuste keskel esineb mittevastavus. Seda näitab ka punktis 7 tehtud globaalne joondamine ja ka DotPlotiga saadud tulemus.
    2. punkti kolmanda järjestuste paari lokaalne joondamine:
    ########################################
    # Program: water
    # Rundate: Wed Mar 07 18:22:06 2007
    # Align_format: srspair
    # Report_file: /ebi/extserv/old-work/water-20070307-18220593324593.output
    ########################################
    #=======================================
    # Aligned_sequences: 2
    # 1: EMBOSS_001
    # 2: EMBOSS_001
    # Matrix: EDNAFULL
    # Gap_penalty: 10.0
    # Extend_penalty: 0.5
    # Length: 662
    # Identity: 507/662 (76.6%)
    # Similarity: 507/662 (76.6%)
    # Gaps: 144/662 (21.8%)
    # Score: 2371.5
    #=======================================
    EMBOSS_001 110 ttgatcacttgaactctaaagattttattgggggcaatctccaagaatta 159
    |||||.|.|||||||||||||||||||||.|..||.||| .||
    EMBOSS_001 4 ttgatgatttgaactctaaagattttattcgtagcgatc--------gta 45
    EMBOSS_001 160 tggaaag--------agttgttaggtaaaaatagggatgatgctatcgtt 201
    ..||..| |||||||||||||||||||||||||||||||||||
    EMBOSS_001 46 gcgatcgatcgcgccagttgttaggtaaaaatagggatgatgctatcgtt 95
    EMBOSS_001 202 aaggcaattacaactgactatgacgcttacaaacaagcgcataagcctcc 251
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 96 aaggcaattacaactgactatgacgcttacaaacaagcgcataagcctcc 145
    EMBOSS_001 252 ttatcaaaaactgttgattacagaagtgaactcttgtcttgaacagttg- 300
    |||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 146 ttatcaaaaactgttgattacagaagtgaactcttgtcttgaacagttga 195
    EMBOSS_001 301 --------------------aaaaaacaaggtatcaaactggctgtggca 330
    ||||||||||||||||||||||||||||||
    EMBOSS_001 196 ggaattatttttgatatggaaaaaaacaaggtatcaaactggctgtggca 245
    EMBOSS_001 331 tcaaactcgaagcgtcaggatgttttgttggcgttggagacaacgcaaat 380
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 246 tcaaactcgaagcgtcaggatgttttgttggcgttggagacaacgcaaat 295
    EMBOSS_001 381 aaaagattattttgaaataatcctagcgcgtgaagatgtttctagaggca 430
    ||||||||||||||||||||||| |||||
    EMBOSS_001 296 aaaagattattttgaaataatcc----------------------aggca 323
    EMBOSS_001 431 aaccttatccagatatttataataaagcagtacaaaaactaggattacaa 480
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 324 aaccttatccagatatttataataaagcagtacaaaaactaggattacaa 373
    EMBOSS_001 481 aaaaaacaactgcttgtagtagaagacagccaaaaaggcattgctgccgc 530
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 374 aaaaaacaactgcttgtagtagaagacagccaaaaaggcattgctgccgc 423
    EMBOSS_001 531 taaagcagccaatctgacagtttttgccattaccgacta----------- 569
    |||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 424 taaagcagccaatctgacagtttttgccattaccgactataacggtgttt 473
    EMBOSS_001 570 -------------------------------------------------- 569
    EMBOSS_001 474 tatttgatacagaacctttttatctgaggcgacgagaagatttttttaag 523
    EMBOSS_001 570 ------------------------ccgatatggcattgatcagagtcaag 595
    ||||||||||||||||||||||||||
    EMBOSS_001 524 acaaagggaattcccattgatcacccgatatggcattgatcagagtcaag 573
    EMBOSS_001 596 ctgatcacaagatagatcatttaggacaactgtgtgtaaaaatcggttgt 645
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 574 ctgatcacaagatagatcatttaggacaactgtgtgtaaaaatcggttgt 623
    EMBOSS_001 646 tttggatcgtga 657
    ||||||||||||
    EMBOSS_001 624 tttggatcgtga 635
    #---------------------------------------
    #---------------------------------------
    Lokaalse joondamise puhul on järjestuste identsus kõrgem kui globaalse joondamise puhul. Paistab, et DotPlot näitab natuke rohkem mittevastavusi kui EMBOSS.
    2. punkti neljanda järjestuste paari lokaalne joondamine:
    ########################################
    # Program: water
    # Rundate: Wed Mar 07 18:24:46 2007
    # Align_format: srspair
    # Report_file: /ebi/extserv/old-work/water-20070307-18244545482145.output
    ########################################
    #=======================================
    # Aligned_sequences: 2
    # 1: EMBOSS_001
    # 2: EMBOSS_001
    # Matrix: EDNAFULL
    # Gap_penalty: 10.0
    # Extend_penalty: 0.5
    # Length: 788
    # Identity: 507/788 (64.3%)
    # Similarity: 507/788 (64.3%)
    # Gaps: 262/788 (33.2%)
    # Score: 2157.0
    #=======================================
    EMBOSS_001 1 atgttgatgattaaaggaattatttttgatatggacggtgttttatttga 50
    |||||||||
    EMBOSS_001 1 atgttgatg----------------------------------------- 9
    EMBOSS_001 51 tacagaacctttttatctgaggcgacgagaagatttttttaagacaaagg 100
    |||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 10 -------cctttttatctgaggcgacgagaagatttttttaagacaaagg 52
    EMBOSS_001 101 gaattcccattgatcacttgaactct----aaagattttat-----tg-- 139
    |||||||||||||||||||||| | |||.|...||| ||
    EMBOSS_001 53 gaattcccattgatcacttgaa---tgaaaaaacaaggtatcaaactggc 99
    EMBOSS_001 140 -ggggcaatctccaagaattatggaaagagttgttaggtaaaaataggga 188
    |.|||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 100 tgtggcaatctccaagaattatggaaagagttgttaggtaaaaataggga 149
    EMBOSS_001 189 tgatgctatcgttaaggcaattacaactgactatgacgcttacaaacaag 238
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 150 tgatgctatcgttaaggcaattacaactgactatgacgcttacaaacaag 199
    EMBOSS_001 239 cgcataagcctccttatcaaaa------------actgtt-gattacaga 275
    |||||||||| .||.||| ||.||| ..|||||||
    EMBOSS_001 200 cgcataagcc-----ctctaaagattttattgggacagttcctttacaga 244
    EMBOSS_001 276 agtgaactcttgtcttgaacagttgaaaaaacaaggtatcaaactggctg 325
    ||||||||||||||||||
    EMBOSS_001 245 agtgaactcttgtcttga-------------------------------- 262
    EMBOSS_001 326 tggcatcaaactcgaagcgtcaggatgttttgttggcgttggagacaacg 375
    |||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 263 -ggcatcaaactcgaagcgtcaggatgttttgttggcgttggagacaacg 311
    EMBOSS_001 376 caaataaaagattattttgaaataatcctagcgcgtgaa-gatgtttcta 424
    |||||||||||||||||||.|.||| || ||| .||.|||
    EMBOSS_001 312 caaataaaagattattttgtattaa----ag-----gaattattttt--- 349
    EMBOSS_001 425 gaggcaaaccttatccagatat--------ttataataaagcagtacaaa 466
    ||||| ||.||.|..| ||||.|
    EMBOSS_001 350 -----------------gatatggacggtgttttatttga----tacaga 378
    EMBOSS_001 467 aactaggattacaaaaaaaacaactgcttgtagtagaagacagccaaaaa 516
    | ||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 379 a---------acaaaaaaaacaactgcttgtagtagaagacagccaaaaa 419
    EMBOSS_001 517 ggcattgctgccgctaaagcagc----------------caatctgac-- 548
    ||||||||||||||||||||||| |||||||||
    EMBOSS_001 420 ggcattgctgccgctaaagcagctatcaaaaactgttgacaatctgacaa 469
    EMBOSS_001 549 -------------------------------------------------- 548
    EMBOSS_001 470 ataatcctagcgcgtgaagatgtttctagaggcaaaccttatccagatat 519
    EMBOSS_001 549 -----------------------------agtttttgccattaccgacta 569
    |||||||||||||||||||||
    EMBOSS_001 520 ttataataaagcagtacaaaaactaggatagtttttgccattaccgacta 569
    EMBOSS_001 570 ccgatatggcattgatcagagtcaagctgatcacaagatagatcatttag 619
    ||||||||||||||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 570 ccgatatggcattgatcagagtcaagctgatcacaagatagatcatttag 619
    EMBOSS_001 620 gacaactgtgtgtaaaaatcggttgttttggatcgtga 657
    ||||||||||||||||||||||||||||||||||||||
    EMBOSS_001 620 gacaactgtgtgtaaaaatcggttgttttggatcgtga 657
    #---------------------------------------
    #---------------------------------------
    Nii EMBOSS kui ka DotPlot näitavad, et tegemist on suhteliselt segase järjestusega, millest on raske midagi konkreetset välja lugeda.
    6. punkti kontroll:
    ########################################
    # Program: water
    # Rundate: Tue Mar 06 06:59:31 2007
    # Align_format: srspair
    # Report_file: /ebi/extserv/old-work/water-20070306-06592972132342.output
    ########################################
    #=======================================
    # Aligned_sequences: 2
    # 1: EMBOSS_001
    # 2: EMBOSS_001
    # Matrix: EBLOSUM62
    # Gap_penalty: 10.0
    # Extend_penalty: 0.5
    # Length: 5
    # Identity: 5/5 (100.0%)
    # Similarity: 5/5 (100.0%)
    # Gaps: 0/5 ( 0.0%)
    # Score: 30.0
    #=======================================
    EMBOSS_001 2 CGTGA 6
    |||||
    EMBOSS_001 1 CGTGA 5
    #---------------------------------------
    #---------------------------------------
    Järeldus: 6. punktis tehtud töö on õige, kuna sain samade parameetritega sama vastuse.
  • Vasakule Paremale
    Bioinformaatika ülesanded #1 Bioinformaatika ülesanded #2 Bioinformaatika ülesanded #3 Bioinformaatika ülesanded #4 Bioinformaatika ülesanded #5 Bioinformaatika ülesanded #6 Bioinformaatika ülesanded #7 Bioinformaatika ülesanded #8 Bioinformaatika ülesanded #9 Bioinformaatika ülesanded #10 Bioinformaatika ülesanded #11 Bioinformaatika ülesanded #12 Bioinformaatika ülesanded #13 Bioinformaatika ülesanded #14 Bioinformaatika ülesanded #15 Bioinformaatika ülesanded #16 Bioinformaatika ülesanded #17 Bioinformaatika ülesanded #18 Bioinformaatika ülesanded #19 Bioinformaatika ülesanded #20 Bioinformaatika ülesanded #21 Bioinformaatika ülesanded #22 Bioinformaatika ülesanded #23 Bioinformaatika ülesanded #24
    Punktid 100 punkti Autor soovib selle materjali allalaadimise eest saada 100 punkti.
    Leheküljed ~ 24 lehte Lehekülgede arv dokumendis
    Aeg2012-11-01 Kuupäev, millal dokument üles laeti
    Allalaadimisi 36 laadimist Kokku alla laetud
    Kommentaarid 0 arvamust Teiste kasutajate poolt lisatud kommentaarid
    Autor Mumm Õppematerjali autor
    Järjestuste paaride joondamine (dot-plot, dünaamiline programmeerimine, skoorid).

    Kasutatud allikad

    Sarnased õppematerjalid

    Molaarmassi krüoskoopiline määramine
    102
    xls

    Molaarmassi krüoskoopiline määramine

    Time Channel 1 Seconds °C 0 12,62 1 12,6 24 2 12,57 22 3 12,53 4 12,5 20 5 12,47 18 16 6 12,43 14 7 12,4 12 8 12,36 10 9 12,33 t,C 8 10 12,29 11 12,26 6 12 12,24 4 13 12,2 14 12,16 2 15 12,13 0 16 12,1 0 200 400 600 800 1000 1200 14 17 12,07 -2 18 12,03 19 12 -4 20 11,

    Füüsikaline ja kolloidkeemia
    Programmeerimiskeel
    555
    doc

    Programmeerimiskeel

    tutvu lausearvutuse keskkonnaga: http://logik.phl.univie.ac.at/~chris/gateway/formular-uk-zentral.html Millistel muutuja väärtustel on lause (Av(B&A))v(-A&(Cv(B&-C))) väär? Panna tuleb results only, 0 on väär 1 on õige Tutvu ajalooga saidis kuni II maailmasõda: http://www.maxmon.com/history.htm Loe läbi jutt ja proovi andmetega mängida: http://math.hws.edu/TMCM/java/DataReps/index.html Kahend süsteemi arvu(101101001) ->kümnend süsteemiks. Nr sisse ja bianarile punkt, ja vaatan base ten integeri kümnendarvudest annab Ecki appletis juuresoleva graafilise kujutise, teen kujundi ja vaatan base integeri mis vastab kahendsüsteemi arvule 1110001 ASCII tabelis? Nr sisse ja punkt bianari, vaatan ...teksti Kümnendsüsteemi arv 33 on kahendsüsteemis? 33 kirjutan ja Base-ten integer, vaatan bianary Loe läbi jutud Atbashi ja Caesari šifri (Caesar cipher) kohta: http://www.wikipedia.org 2 Tutvu ajalooga kuni 1970ndad: http://www.islandnet.com/~kpolsson/comphist/ 47-68 ingli

    Infotehnoloogia
    BIOinformaatika kodutöö 5
    79
    doc

    BIOinformaatika kodutöö 5

    Bioinformaatika 5 Andmebaasid (KEGG, NCBI, RCSB), järjestuste (SMS, BioEdit) ja struktuuride (SPdbV) analüüs 1. KEGG-i kasutamine (http://www.genome.jp/ a. Leida liikide Escherichia coli K12 MG1655, Drosophila melanogaster ja Homo sapiens glükolüüsi rajad ning ensüümid aldolaas ja püruvaatkinaas. Escherichia coli glükolüüsi rada: http://www.kegg.com/dbget-bin/get_pathway?org_name=eco&mapno=00010 Drosophila glükolüüsi rada: http://www.kegg.com/dbget-bin/get_pathway?org_name=dme&mapno=00010 Homo sapiens glükolüüsi rada: http://www.kegg.com/dbget-bin/get_pathway?org_name=hsa&mapno=00010 aldodaas: http://www.kegg.com/dbget-bin/www_bget?enzyme+4.1.2.13 püruvaatkinees: http://www.kegg.com/dbget-bin/www_bget?enzyme+2.7.1.40 b. Leida vastavad geenid ­ KEGG-i entry numbrid, geeni nimed, nukleotiidsed järjestused ning asukohad geenikaardil. Aldolaas : Escherichia coli K12 MG1655: http://www.kegg.com/dbget-

    Bioinformaatika
    Exceli-kodutöö
    262
    xls

    Exceli-kodutöö

    Teravilja Kartuli Min. Piima lehma saak saak väetisi/ha Lehmade kohta aastas Sigade Maakond Majand Aasta (ts/ha) (ts/ha) (kg) arv (kg) arv Harju Aasmae 83 25 141 318 809 3404 1170 Harju Alavere 83 31 187 279 924 3600 3595 Harju Arukyla 83 22 155 196 1707 3637 3692 Harju Habaja 83 21 133 177 1267 2877 4087 Harju Haiba 83 25 141 245 919 3354 2920 Harju Kehra 83 21 126 296 1555 3211 1380 Harju Koidula 83 23 173 204 638 3435 1661 Harju Kungla 83 20 91 231 837 3245 1244 Harju

    Arvuti
    Liha töötlemine
    1168
    pdf

    Liha töötlemine

    Handbook of Meat Processing Handbook of Meat Processing Fidel Toldrá EDITOR A John Wiley & Sons, Inc., Publication Edition first published 2010 © 2010 Blackwell Publishing Blackwell Publishing was acquired by John Wiley & Sons in February 2007. Blackwell’s publishing program has been merged with Wiley’s global Scientific, Technical, and Medical business to form Wiley-Blackwell. Editorial Office 2121 State Avenue, Ames, Iowa 50014-8300, USA For details of our global editorial offices, for customer services, and for information about how to apply for permission to reuse the copyright material in this book, please see our website at www.wiley.com/ wiley-blackwell. Authorization to photocopy items for internal or personal use, or the internal or personal use of specific clients, is granted by Blackwell Publishing, provided that the base fee is paid directly to the Copyright Clearance Center, 222 Rosewood Drive, Danvers, MA 01923. F

    Inglise keel
    THE- PSYCHOLOGY OF COMMUNICATION
    297
    pdf

    THE PSYCHOLOGY OF COMMUNICATION

    W. Lambert Gardiner has been leading his life in neat, The Psychology of Communications multiple-of-five-year installments for the convenience of biographers. VOLUME 1 1935-1955 GROWING IN SCOTLAND Flunked out of elementary school, High School, and Glasgow University. The Psychology of VOLUME 2 1955-1960 STUDYING IN CANADA Communication Work by day and study by night. B. A. Sir George Williams University. High School Teaching Diploma McGill University. VOLUME 3 1960-1965 STUDYING IN USA Ph. D. Cornell University. Nothing else happened. VOLUME 6 1980-1985 VOLUME 4 1965-1970

    Psüholoogia
    Fitness In Soccer
    409
    pdf

    Fitness In Soccer

    [email protected] 06 Aug 2018 FITNESS IN SOCCER THE SCIENCE AND PRACTICAL APPLICATION Jan Van Winckel, Werner Helsen, Kenny McMillan, David Tenney, Jean-Pierre Meert, Paul Bradley [email protected] 06 Aug 2018 Isbn-number : 9789082132304 Publisher: Moveo Ergo Sum / Klein-Gelmen Proofreading: Jim Newall Quill Content |Writing, Editing and Web site services http://www.quillsites.co.uk Photos: Jean Leemans and Etienne Claessens Cover and lay-out: Dots & Bits © 2014 Jan Van Winckel Printed and bound at Manipal Technologies Ltd., India All rights reserved. No pa

    Kategoriseerimata
    Christopher Vogler The Writers Journey
    904
    pdf

    Christopher Vogler The Writers Journey

    THE W R I T E R ' S JOURNEY M Y T H I C STRUCTURE FOR W R I T E R S THIRD EDITION CHRISTOPHER VOGLER S C R E E N W R I T I N G / W R I T I N G Christopher Vogler explores the powerful relationship between mythology and storytelling in his clear, concise style that's made i this book required reading for movie executives, screenwriters, playwrights, fiction and non-fiction writers, scholars, and fans of pop culture all over the world. Discover a set of useful myth-inspired storytelling paradigms like "The Hero's Journey," and step-by-step guidelines to plot and • character development. Based on the work of Joseph Campbell, The Writers Journey is a must for all writers interested

    Ingliskeelne kirjandus




    Meedia

    Kommentaarid (0)

    Kommentaarid sellele materjalile puuduvad. Ole esimene ja kommenteeri



    Sellel veebilehel kasutatakse küpsiseid. Kasutamist jätkates nõustute küpsiste ja veebilehe üldtingimustega Nõustun