59. Seed & Extend
Good alignments must have significant
exact alignment
Minimal exact alignment length = l/(k+1)
60. Seed & Extend
Good alignments must have significant
exact alignment
Minimal exact alignment length = l/(k+1)
Expensive to scale
61. Seed & Extend
Good alignments must have significant
exact alignment
Minimal exact alignment length = l/(k+1)
Expensive to scale
62. Seed & Extend
Good alignments must have significant
exact alignment
Minimal exact alignment length = l/(k+1)
Expensive to scale
Need parallelization framework
68. Bowtie: Ultrafast short read aligner
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human
genome. Genome Biol 10 (3): R25.
69. SOAPSnp: Consensus alignment and SNP calling
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human
genome. Genome Biol 10 (3): R25.
70. Crossbow: Rapid whole genome SNP analysis
Ben Langmead
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human
genome. Genome Biol 10 (3): R25.
78. Estimating relative evolutionary rates
from sequence comparisons:
Identification of probable orthologs
Admissible comparisons: A or B vs. D
C vs. E
Inadmissible comparisons: A or B vs. E
C vs. D
A B C D E species tree
gene tree
S. cerevisiae C. elegans
79. Estimating relative evolutionary rates
from sequence comparisons:
1. Orthologs found using the Reciprocal
smallest distance algorithm
2. Build alignment between two orthologs
>Sequence C
MSGRTILASTIAKPFQEEVTKAVKQLNFT-----PKLVGLLSNEDPAAKMYANWTGKTCESLGFKYEL-…
>Sequence E
MSGRTILASKVAETFNTEIINNVEEYKKTHNGQGPLLVGFLANNDPAAKMYATWTQKTSESMGFRYDL…
3. Estimate distance given a substitution
matrix
Phe Ala Pro Leu Thr
Phe
Ala µπ
Pro µπ µπ µπ
Leu µπ µπ µπ µπ
A B C D E species tree
gene tree
S. cerevisiae C. elegans
80. RSD algorithm summary
Genome I Genome J
Ib Jc
Align sequences &
Calculate distances L Orthologs:
Align sequences &
Calculate distances H
ib - jc D = 0.1
c
vs. D=1.2 vs. D=0.2
a b a
vs. D=0.1 vs. D=0.3
c b b b
vs. D=0.9 vs. D=0.1
c c b c
82. Roundup is a database of orthologs
and their evolutionary distances.
To get started, click browse. Alternatively, you can
read our documentation here.
Good luck, researchers!