ISMB/ECCB 2019 読み会

論文紹介 (https://academic.oup.com/bioinformatics/article/35/14/i71/5529231)

Transcript

1. 
   Efficient merging of genome profile alignments ISMB / ECCB 2019  @  
     @ocxtal
2. • WK? • André Hennig and Kay Nieselt • Eberhard Karls Univ., Tübingen (3%/) • "i]? • Multiple Whole-Genome Alignment (MWGA) ! Geg @ 49:)0$.&!X> • U  MWGA bV!hO_YM MWGA
   \@ – DS MWGA #;':*8 =Md • g  • (<5;^_ (1,HQ)  MWGA ?Bg @    ← "I • g   • `JY GPa[R  • X>L_FAE  • 6<-7&R • ZCTNDSL_
   c1,+.2 f^
3. pairwise local alignment: •  %
   local alignment 1" whole-genome alignment (WGA): • #
   local alignment  multiple whole-genome alignment (MWGA): • WGA! & • multiple global alignment (clustal  MAFFT ) 
   $ Paten et al., 2008 BLAST, BLAT, LAST   $
4. MWGA: pairwise alignment :# #  • ?/;; 6)<, &3*;: pairwise alignment 6)<, MWGA 9!%0. greedy #-  • N1" +2(7  5 *;: MWGA
   MWGA • alignment 6)
    consensus 8@6)MWGA '4 A B C D E F A B C ... Paten et. al., 2011 $MWGA  &3>=
5. • pairwise alignment B6I8+90=&%"C... • consensusB6 alignment 5 2 alignment B6!
    → SuperGenome 
   3< • alignment ,$"2EK (/>) index H7 → ' 2 { EK, $#' } $"F; G:@-J 2(/ A?  • .1 ;4!
   *D 
6. • progressiveMauve (PM) )%! 1'
   GPA &/>D • simulated genome • Bordetella pertussis C3#+-0#.1 (EVOLVER)  N : genome >D • real dataset • K. pneumoniae  S. aureus  160+ :"(,*$ PC: MWGS K22LP6 alignment set @B 
    set 2LP68?  pairwise WGS   consistent ; progressiveMauve (PM)  
   FG: MWGS <D  4 local alignment 9 NE8? AM= (NE5F?) JO7; → PC JHI FG: PM MWGS<D  4 local alignment  → AM=
7. • u\
   SuperGenome21Oc$UN€ alignment qV$7-
   MWGA$QdIT !! ↑  _DMWGA^ MWGAwF! IT).3`p5:=.€nK! • SuperGenome 21OcZeIT).3iLz[lPJ# • Y21OcAGk> "!? [~]m] • MWGA $wFB xy$|R! Ze{s • B !+&/}hf%<*;/8$bI! ga# • Cactus (pCactus), Enredo, Pecan, TBA, Multiz 
   Ybj}h$B %<*;/8tE •  pMauve  €X...... • ,9'-9'5( human !? • vS?oWOc;63r‚@H!K • (human  simulated genome €) • 0.)4MC "
8. • 
   • D. Earl et al. (2014), Alignathon: A competitive assessment of whole genome alignment methods. • B. Kehr et al. (2014), Genome alignment with graph data structures: a comparison. • M Blanchette et al. (2004), Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner. • A. E. Darling et al. (2004), Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements. • A. E. Darling et al. (2010), progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement. • B. Paten et al. (2011), Cactus: Algorithms for genome multiple sequence alignment.