Proceedings of the National Academy of Sciences,
Journal Year:
2017,
Volume and Issue:
114(35)
Published: Aug. 15, 2017
Significance
CRISPR-Cas
is
an
adaptive
immunity
system
that
protects
bacteria
and
archaea
from
mobile
genetic
elements.
We
present
comparative
genomic
phylogenetic
analysis
of
minimal
variants
associated
with
distinct
families
transposable
elements
develop
the
hypothesis
such
repurposed
defense
systems
contribute
to
element
propagation
by
facilitating
transposition
into
specific
sites.
Thus,
these
are
predicted
propagate
via
RNA-guided
transposition,
a
mechanism
has
not
been
previously
described
for
DNA
transposons.
Science,
Journal Year:
2018,
Volume and Issue:
362(6416), P. 839 - 842
Published: Oct. 19, 2018
CRISPR-Cas
systems
provide
microbes
with
adaptive
immunity
to
infectious
nucleic
acids
and
are
widely
employed
as
genome
editing
tools.
These
tools
use
RNA-guided
Cas
proteins
whose
large
size
(950
1400
amino
acids)
has
been
considered
essential
their
specific
DNA-
or
RNA-targeting
activities.
Here
we
present
a
set
of
from
uncultivated
archaea
that
contain
Cas14,
family
exceptionally
compact
nucleases
(400
700
acids).
Despite
small
size,
Cas14
capable
targeted
single-stranded
DNA
(ssDNA)
cleavage
without
restrictive
sequence
requirements.
Moreover,
target
recognition
by
triggers
nonspecific
cutting
ssDNA
molecules,
an
activity
enables
high-fidelity
single-nucleotide
polymorphism
genotyping
(Cas14-DETECTR).
Metagenomic
data
show
multiple
CRISPR-Cas14
evolved
independently
suggest
potential
evolutionary
origin
single-effector
CRISPR-based
immunity.
BMC Bioinformatics,
Journal Year:
2019,
Volume and Issue:
20(1)
Published: Sept. 14, 2019
HH-suite
is
a
widely
used
open
source
software
suite
for
sensitive
sequence
similarity
searches
and
protein
fold
recognition.
It
based
on
pairwise
alignment
of
profile
Hidden
Markov
models
(HMMs),
which
represent
multiple
alignments
homologous
proteins.We
developed
single-instruction
multiple-data
(SIMD)
vectorized
implementation
the
Viterbi
algorithm
HMM
introduced
various
other
speed-ups.
These
accelerated
search
methods
HHsearch
by
factor
4
HHblits
2
over
previous
version
2.0.16.
HHblits3
∼10×
faster
than
PSI-BLAST
∼20×
HMMER3.
Jobs
to
perform
with
many
query
HMMs
can
be
parallelized
cores
cluster
servers
using
OpenMP
message
passing
interface
(MPI).
The
free,
open-source,
GPLv3-licensed
available
at
https://github.com/soedinglab/hh-suite
.The
added
functionalities
increased
speed
should
facilitate
their
use
in
large-scale
structure
function
prediction,
e.g.
metagenomics
genomics
projects.
Science,
Journal Year:
2018,
Volume and Issue:
363(6422), P. 88 - 91
Published: Dec. 7, 2018
Additional,
diverse
CRISPR
systems
have
been
revolutionizing
molecular
biology.
Mining
the
metagenomic
database,
Yan
et
al.
systematically
discovered
additional
subtypes
of
type
V
CRISPR-Cas
systems.
The
Cas12
effectors
displayed
a
range
activities,
including
target
and
collateral
cleavage
single-stranded
RNA
DNA,
as
well
double-stranded
DNA
nicking
cleavage.
These
nuclease
activities
suggest
how
an
ancient
transposase
may
evolved
into
various
expand
nucleic
acid
detection
genome-editing
toolbox.
Science
,
this
issue
p.
88
