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

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。

Yuki_Hamaguchi

August 18, 2018
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  1. 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
  2. ᶃ3/"४࠷దߏ଄Λ༻͍ͯ ɹҎ্ͷਖ਼ղԘجର਺ ɹΛ࣋ͭ୅දతͳ3/"ߏ଄ ɹΛग़ྗ͢Δ ࣗ ༝ Τ ω ϧ Ϊ

    | ૯߹Ԙجରܗ੒Ґஔڑ཭ BMJ'SFF'PMEͷڧΈ ̏ 41"34&   5VSCP'PMEJJ  ᶄ࣌ؒܭࢉྔ͕௿͍ ɹΞϥΠϝϯτϑϦʔख๏ ɹैདྷΑΓ଎౓ɾਫ਼౓ ɹͷόϥϯε͕ྑ͍ 3/"४࠷ద TVCPQUJNBM ߏ଄ ʼ IUUQTPQFOXFUXBSFPSHXJLJ 8JLJPNJDT3/"@TFDPOEBSZ@TUSVDUVSF@QSFEJDUJPO  .94$"3/"  Ex) Saccharomyces cerevisiaeͷU3/" 1IF
  3. 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
  4. S3/" U3/" άϧʔϓᶘΠϯτϩϯ 6TO3/" 3/BTF1 UN3/" 4&$*4ʜ 5SFOET#JPDIFN4DJ QQr 

    IUUQSOBVDTDFEVSOBDFOUFS SJCPTPNF@JNBHFTIUNM *6#.#-JGF     Џ༧ଌߏ଄಺Ͱ߹கͨ͠Ԙجର਺ ൺֱ͢Δ༧ଌπʔϧɹ(7ͭ) 3/"DBTU  طଘͷΞϥΠϝϯτϑϦʔख๏ 3/"TQB  .94$"3/"   $FOUSPJE'PME  3/"BMJGPME   41"34&  5VSCP'PMEJJ  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/ '/
  5. ೋ࣍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
  6. 3/"ೋ࣍ߏ଄༧ଌޮ཰  ฏۉԘج਺ OU ࣌ ؒ (log) ୯Ґ͸ඵ "MJ'SFF'PME 3/"BMJGPME

    $FOUSPJE'PME 5VSCPGPMEJJ "MJ'SFF'PME͸$FOUSPJE'PME΍5VSCPGPMEͱ ಉ౳ͷ଎͍ղੳ଎౓Λ༗͍ͯ͠Δ 3/"BMJGPMEʹରͯ͠ ͸ྼ͍ͬͯΔ ➕ *ཧ࿦࣌ؒܭࢉྔ O(al2+mn),O(al4+mn) B૬ಉԘجର਺ NϞνʔϑ਺ɺO഑ྻ௕ O(l2),O(l4)͸3/"TVCPQU
  7. 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    
  8.  ίϝϯτ Cell, Vol. 113, 383–394, May 2, 2003, 7MPPQͷΑ͏ͳߏ଄ϞνʔϑΛ

    ଞͷU3/"σʔλͰ͸ڞ༗͍͕ͯͨ͠ɺ ग़ྗ͞Εͨ୅දߏ଄ͷΈ ͦͷϞνʔϑΛอ༗͍ͯ͠ͳ͔ͬͨ Մೳੑ͕͋ΔͷͰ͸ʁ