aliFreeFold: an alignment-free approach to predict secondary structure from homologous RNA sequences

ISMB読み会2018で紹介したaliFreeFoldに関する発表スライドです。

Transcript

1. BMJ'SFF'PME
   dΞϥΠϝϯτϑϦʔͳ
   3/"ೋ࣍ߏ଄༧ଌख๏d ঺հऀɿ඿ޱ༔و
   ౦ژେֶେֶӃ৽ྖҬ૑੒ՊֶݚڀՊ ϝσΟΧϧ৘ใੜ໋ઐ߈ ؠ࡚ݚڀࣨ M2 *4.#
   +PVSOBM
2. ࣗݾ঺հ ௚ۙͰࢀՃ͢Δֶձɾݚڀձ
   ɹɾ೔ຊਐԽֶձ
   ɹ
   ɹɾੜ໋ͷىݯٴͼਐԽֶձ
   
   Նͷֶߍ ڵຯ͋Δ෼໺
   ɹਅ֩ੜ෺ͷىݯ ಛʹϛτίϯυϦΞ ೔ຊਐԽֶձཁࢫू
   1 ̍
3. 3/"ೋ࣍ߏ଄༧ଌͷΞϓϩʔν ᶃҰͭͷ3/"Ԙج഑ྻ͔Β༧ଌ ᶄ૬ಉ3/"Ԙج഑ྻ͔Β༧ଌ ࠷খࣗ༝ΤωϧΪʔߏ଄ମ .'&
   Λࢉग़ ίϯηϯαεͳೋ࣍ߏ଄Λࢉग़ ૯߹Ԙجରܗ੒Ґஔڑ཭ ࣗ ༝ Τ ω ϧ Ϊ | Methods 103 (2016) 86–98 ૬ಉ3/"ͦΕͧΕΛൺֱ͠ɺ
   ೋ࣍ߏ଄ͷอଘੑΛݕग़ ࣗ༝ΤωϧΪʔύϥϝʔλʹج͖ͮɺ ೋ࣍ߏ଄ީิΛ໢ཏతʹ୳ࡧɾධՁ ̎ MJGFTDJFODFECKQIPVLPLVQEG#@pOBMQEG BMJ'SFF'PME
4. ᶃ3/"४࠷దߏ଄Λ༻͍ͯ
   ɹҎ্ͷਖ਼ղԘجର਺
   ɹΛ࣋ͭ୅දతͳ3/"ߏ଄
   ɹΛग़ྗ͢Δ ࣗ ༝ Τ ω ϧ Ϊ | ૯߹Ԙجରܗ੒Ґஔڑ཭ BMJ'SFF'PMEͷڧΈ ̏ 41"34&
   
   
   
   
   
   
   
   
   5VSCP'PME
   JJ
   
   
    ᶄ࣌ؒܭࢉྔ͕௿͍
   ɹΞϥΠϝϯτϑϦʔख๏
   ɹ
   ैདྷΑΓ଎౓ɾਫ਼౓
   ɹ
   
   ͷόϥϯε͕ྑ͍ 3/"४࠷ద TVCPQUJNBM ߏ଄ ʼ IUUQTPQFOXFUXBSFPSHXJLJ
   8JLJPNJDT3/"@TFDPOEBSZ@TUSVDUVSF@QSFEJDUJPO  .94$"3/"
   
    Ex) Saccharomyces cerevisiaeͷU3/"
   1IF
5. BMJ'SFF'PMEͷΞϓϩʔνख๏ᶃ input: ૬ಉRNA഑ྻ ̐ :@
   "$$6"$66("$6$"($((66"("(6"6
   $($666$"6"$(($("("(6$"66((6
   6$"""6$$""6"(6"((6"
   "'@
   (((($$66"($6$"($6((("("($($
   $6($666($"$($"(("((6$"($((6
   6$("6$$$($6"(($6$$"
   "+@
   6$$6$"(6"($6$"(6((6"("($((6
   $(($6(66""$$("66((6$(6"((66
   $(""6$$6"$66(((("(
   9@
   "$$6"$66""$6$"(6((66"("(6"$
   6($666$"6"$(($((("(($"66((6
   6$"""6$$""6"(6"((6"
   7@
   "$6666"""(("6"(6"(666"6$$(6
   6((6$66"((""$$""""""66((6($
   ""$6$$"""6""""(6" ᶃ֤૬ಉ3/"഑ྻͷ४࠷దߏ଄Λ3/"TVCPQU Λ༻͍ͯࢉग़
   ᶄۙྡϞνʔϑߏ଄ ʢϚϧνϧʔϓɾεςϜ౳ʣͷ਺Λࢉग़ ۙྡϞνʔϑߏ଄ଞʹ΋ϔΞϐϯϧʔϓɺΠϯλʔφϧϧʔϓɺ
   ɹɹɹɹɹɹɹɹɹόϧδɺΤΫελʔφϧϧʔϓ `ɺ` ɺγϡʔυίϯτ 7JFOOB3/"ύοέʔδͷҰͭ
6. BMJ'SFF'PMEͷΞϓϩʔνख๏ᶄ output ୅දߏ଄ ̑ ᶅϞνʔϑ͝ͱʹอଘࢦ਺Λܭࢉɹ Τϯτϩϐʔܭࢉ
   ᶆ֤Ϟνʔϑͷอଘࢦ਺ʹॏΈ͚ͮ
   ʢอଘࢦ਺ʹ࠷େείΞΛ͔͚Δʣ
   ᶇ֤Ϟνʔϑͷอଘࢦ਺͔Βશ૬ಉ3/"ͷॏ৺తߏ଄Λࢉग़
   ᶈ֤૬ಉ3/"ͷதͰॏ৺తߏ଄ʹ͍ۙ΋ͷΛநग़
7. S3/"
   U3/" άϧʔϓᶘΠϯτϩϯ
   6
   TO3/"
   3/BTF1
   UN
   3/" 4&$*4ʜ 5SFOET
   #JPDIFN
   4DJ
   
   QQ
   r
    IUUQSOBVDTDFEVSOBDFOUFS
   SJCPTPNF@JNBHFTIUNM *6#.#
   -JGF
     
    Џ
   ༧ଌߏ଄಺Ͱ߹கͨ͠Ԙجର਺ ൺֱ͢Δ༧ଌπʔϧɹ(7ͭ) 3/"DBTU  
   طଘͷΞϥΠϝϯτϑϦʔख๏
   3/"TQB
   
   
   
   
   
   
   
   
   .94$"3/"
   
   
   $FOUSPJE'PME
   
   3/"BMJGPME
   
   
   
   
   41"34&
   
   
   
   
   
   
   
   
   5VSCP'PME
   JJ
   
   
    Dataset: ط஌ͷ૬ಉRNA഑ྻ σʔληοτͱධՁํ๏  ධՁํ๏: Sensivity, PPV, MCC ਅͷ݁Ռ ରܗ੒
   Ԙج਺ ରඇܗ੒
   Ԙج਺ ରܗ੒
   Ԙج਺ 51 '1 ରඇܗ੒
   Ԙج਺ '/ 5/ ༧
   ଌ
   ݁
   Ռ ✖51 '/
   ˓5/ '/
8. ೋ࣍ߏ଄༧ଌͷਖ਼ղԘجର਺ ̓ ฏ ۉ ਖ਼ ղ ਺ ׂ ߹ (%) ݸ M F E ݸ ݸ
   c
   ݸ ̍ݸ ४࠷దߏ଄σʔλ਺ .'&ߏ଄ΑΓ΋४࠷దߏ଄ͷํ͕Ԙجର਺Λਖ਼͘͠༧ଌͰ͖Δ
   ४࠷దߏ଄σʔλ਺͕૿Ճ͢Δ΄Ͳ༧ଌੑೳ্͕ঢ͢Δ
9. 3/"ೋ࣍ߏ଄༧ଌੑೳᶃ ̔ ᶃ"MJ'SFF'PME͸3/"DBTUΑΓ΋.$$ 117 4&/4શͯͰ༏Ε͍ͯΔ
   ᶄ"MJ'SFF'PMEͱ5VSCP'PME
   ᶘ͕࠷ྑͷ༧ଌπʔϧͰ͋Δ ධՁࢦඪ ର৅σʔληοτ
   
   OD3/"
   GBNJMZ
10. ̕ ૬ಉ3/"਺ "MJ'SFF'PME͸σʔληοτ਺Λ૿Ճͤ͞Δͱ
    ͞Βʹ༧ଌೳྗ্͕ঢ͢Δ 3/"ೋ࣍ߏ଄༧ଌੑೳᶄ
11. 3/"ೋ࣍ߏ଄༧ଌޮ཰  ฏۉԘج਺ OU ࣌ ؒ (log) ୯Ґ͸ඵ "MJ'SFF'PME 3/"BMJGPME $FOUSPJE'PME 5VSCPGPME
    JJ "MJ'SFF'PME͸$FOUSPJE'PME΍5VSCPGPMEͱ
    ಉ౳ͷ଎͍ղੳ଎౓Λ༗͍ͯ͠Δ 3/"BMJGPMEʹରͯ͠
    ͸ྼ͍ͬͯΔ ➕ *ཧ࿦࣌ؒܭࢉྔ
    O(al2+mn),O(al4+mn) B૬ಉԘجର਺
    N
    Ϟνʔϑ਺ɺO
    ഑ྻ௕
    O(l2),O(l4)͸3/"TVCPQU
12. ࠓޙͷओͳվળ఺  ᶃ४࠷దߏ଄ͷܭࢉπʔϧมߋ
    ɹ 3/"TVCPQU  ˠWT@TVCPQU  γϡʔυϊοτߏ଄
    ͷݕग़ਫ਼౓Λ্͛Δ 3/BTF1ͷ༧ଌਫ਼౓Λ
    ͋͛ΒΕΔ ᶄอଘࢦ਺ͷΑΓਖ਼֬ͳܭࢉ 3/"
    
    r ೤ྗֶత౷ܭख๏ͷ׆༻ ଟมྔղੳ
    ˠΑΓద੾ͳ୅දߏ଄ͷݕग़ ࠷ ྑ ४ ࠷ ద ߏ ଄
    ͔ Β ͷ Ԙ ج ର ڑ ཭ .'&
    ͔ΒͷԘجରڑ཭ γϡʔυϊοτߏ଄ .PM
    #JP4ZTU
     
    
    
13.  *RNAfold (web)Λ࢖ͬͯඳը ࣮ࡍʹBMJ'SFF'PMEΛ૸ΒͤͯΈͨ ϚπϤΠάαͷ৭ૉମU3/""TO DG
    U3/"TDBO4&
    ͰͷU3/"ߏ଄༧ଌ αϯϓϧσʔλ U3/"ͷೋ࣍ߏ଄༧ଌ͸ैདྷ๏ΑΓ΋ྑͦ͞͏ʹݟ͑Δ ΞϯνίυϯྖҬ DG
    $FOUSPJE'PME
    ͰͷU3/"ߏ଄༧ଌ
14.  ίϝϯτ Cell, Vol. 113, 383–394, May 2, 2003, 7MPPQͷΑ͏ͳߏ଄ϞνʔϑΛ
    ଞͷU3/"σʔλͰ͸ڞ༗͍͕ͯͨ͠ɺ
    ग़ྗ͞Εͨ୅දߏ଄ͷΈ
    ͦͷϞνʔϑΛอ༗͍ͯ͠ͳ͔ͬͨ
    Մೳੑ͕͋ΔͷͰ͸ʁ