International Journal of Molecular Sciences,
Journal Year:
2022,
Volume and Issue:
23(17), P. 9834 - 9834
Published: Aug. 30, 2022
Whole
genome
sequencing
(WGS)
provides
the
highest
resolution
for
genome-based
species
identification
and
can
provide
insight
into
antimicrobial
resistance
virulence
potential
of
a
single
microbiological
isolate
during
diagnostic
process.
In
contrast,
metagenomic
allows
analysis
DNA
segments
from
multiple
microorganisms
within
community,
either
using
an
amplicon-
or
shotgun-based
approach.
However,
WGS
shotgun
data
are
rarely
combined,
although
such
approach
may
generate
additive
synergistic
information,
critical
for,
e.g.,
patient
management,
infection
control,
pathogen
surveillance.
To
produce
combined
workflow
with
actionable
outputs,
we
need
to
understand
pre-to-post
analytical
process
both
technologies.
This
will
require
specific
databases
storing
interlinked
metadata,
also
involves
customized
bioinformatic
pipelines.
review
article
overview
steps
clinical
application
combining
metagenomics
together
diagnosis.
Nucleic Acids Research,
Journal Year:
2022,
Volume and Issue:
51(D1), P. D733 - D743
Published: Nov. 18, 2022
Viruses
are
widely
recognized
as
critical
members
of
all
microbiomes.
Metagenomics
enables
large-scale
exploration
the
global
virosphere,
progressively
revealing
extensive
genomic
diversity
viruses
on
Earth
and
highlighting
myriad
ways
by
which
impact
biological
processes.
IMG/VR
provides
access
to
largest
collection
viral
sequences
obtained
from
(meta)genomes,
along
with
functional
annotation
rich
metadata.
A
web
interface
users
efficiently
browse
search
based
genome
features
and/or
sequence
similarity.
Here,
we
present
fourth
version
IMG/VR,
composed
>15
million
virus
genomes
fragments,
a
≈6-fold
increase
in
size
compared
previous
version.
These
clustered
into
8.7
operational
taxonomic
units,
including
231
408
at
least
one
high-quality
representative.
Viral
now
systematically
identified
genomes,
metagenomes,
metatranscriptomes
using
new
detection
approach
(geNomad),
IMG
standard
complemented
quality
estimation
CheckV,
classification
reflecting
latest
standards,
microbial
host
taxonomy
prediction.
v4
is
available
https://img.jgi.doe.gov/vr,
underlying
data
download
https://genome.jgi.doe.gov/portal/IMG_VR.
Cell,
Journal Year:
2022,
Volume and Issue:
185(21), P. 4023 - 4037.e18
Published: Sept. 28, 2022
High-throughput
RNA
sequencing
offers
broad
opportunities
to
explore
the
Earth
virome.
Mining
5,150
diverse
metatranscriptomes
uncovered
>2.5
million
virus
contigs.
Analysis
of
>330,000
RNA-dependent
polymerases
(RdRPs)
shows
that
this
expansion
corresponds
a
5-fold
increase
known
diversity.
Gene
content
analysis
revealed
multiple
protein
domains
previously
not
found
in
viruses
and
implicated
virus-host
interactions.
Extended
RdRP
phylogeny
supports
monophyly
five
established
phyla
reveals
two
putative
additional
bacteriophage
numerous
classes
orders.
The
dramatically
expanded
phylum
Lenarviricota,
consisting
bacterial
related
eukaryotic
viruses,
now
accounts
for
third
Identification
CRISPR
spacer
matches
bacteriolytic
proteins
suggests
subsets
picobirnaviruses
partitiviruses,
associated
with
eukaryotes,
infect
prokaryotic
hosts.
Nature Biotechnology,
Journal Year:
2023,
Volume and Issue:
42(8), P. 1303 - 1312
Published: Sept. 21, 2023
Identifying
and
characterizing
mobile
genetic
elements
in
sequencing
data
is
essential
for
understanding
their
diversity,
ecology,
biotechnological
applications
impact
on
public
health.
Here
we
introduce
geNomad,
a
classification
annotation
framework
that
combines
information
from
gene
content
deep
neural
network
to
identify
sequences
of
plasmids
viruses.
geNomad
uses
dataset
more
than
200,000
marker
protein
profiles
provide
functional
taxonomic
assignment
viral
genomes.
Using
conditional
random
field
model,
also
detects
proviruses
integrated
into
host
genomes
with
high
precision.
In
benchmarks,
achieved
performance
diverse
viruses
(Matthews
correlation
coefficient
77.8%
95.3%,
respectively),
substantially
outperforming
other
tools.
Leveraging
geNomad's
speed
scalability,
processed
over
2.7
trillion
base
pairs
data,
leading
the
discovery
millions
are
available
through
IMG/VR
IMG/PR
databases.
at
https://portal.nersc.gov/genomad
.
Nucleic Acids Research,
Journal Year:
2023,
Volume and Issue:
52(D1), P. D33 - D43
Published: Nov. 22, 2023
Abstract
The
National
Center
for
Biotechnology
Information
(NCBI)
provides
online
information
resources
biology,
including
the
GenBank®
nucleic
acid
sequence
database
and
PubMed®
of
citations
abstracts
published
in
life
science
journals.
NCBI
search
retrieval
operations
most
these
data
from
35
distinct
databases.
E-utilities
serve
as
programming
interface
Resources
receiving
significant
updates
past
year
include
PubMed,
PMC,
Bookshelf,
SciENcv,
NIH
Comparative
Genomics
Resource
(CGR),
Virus,
SRA,
RefSeq,
foreign
contamination
screening
tools,
Taxonomy,
iCn3D,
ClinVar,
GTR,
MedGen,
dbSNP,
ALFA,
ClinicalTrials.gov,
Pathogen
Detection,
antimicrobial
resistance
resources,
PubChem.
These
can
be
accessed
through
home
page
at
https://www.ncbi.nlm.nih.gov.
Frontiers in Microbiology,
Journal Year:
2021,
Volume and Issue:
12
Published: March 23, 2021
Metagenomics
is
a
segment
of
conventional
microbial
genomics
dedicated
to
the
sequencing
and
analysis
combined
genomic
DNA
entire
environmental
samples.
The
most
critical
step
metagenomic
data
reconstruction
individual
genes
genomes
microorganisms
in
communities
using
assemblers
–
computational
programs
that
put
together
small
fragments
sequenced
generated
by
instruments.
Here,
we
describe
challenges
assembly,
wide
spectrum
applications
which
assemblies
were
used
better
understand
ecology
evolution
ecosystems,
present
one
efficient
assemblers,
SPAdes
was
upgraded
become
applicable
for
metagenomics.
Nucleic Acids Research,
Journal Year:
2022,
Volume and Issue:
51(D1), P. D957 - D963
Published: Oct. 16, 2022
Abstract
The
Genomes
OnLine
Database
(GOLD)
(https://gold.jgi.doe.gov/)
at
the
Department
of
Energy
Joint
Genome
Institute
(DOE-JGI)
continues
to
maintain
its
role
as
one
flagship
genomic
metadata
repositories
world.
ever-increasing
number
projects
and
are
freely
available
user
community
world-wide.
GOLD’s
is
consumed
by
scientists
remains
an
important
source
for
large-scale
comparative
genomics
analysis
initiatives.
Encouraged
this
active
engagement
growth,
GOLD
has
continued
add
new
components
capabilities.
features
such
a
public
Application
Programming
Interface
(API)
Ecosystem
landing
page
well
growth
different
entities
in
current
v.9
edition
described
detail
manuscript.
Virus Evolution,
Journal Year:
2022,
Volume and Issue:
8(2)
Published: July 1, 2022
Despite
a
rapid
expansion
in
the
number
of
documented
viruses
following
advent
metagenomic
sequencing,
identification
and
annotation
highly
divergent
RNA
remain
challenging,
particularly
from
poorly
characterized
hosts
environmental
samples.
Protein
structures
are
more
conserved
than
primary
sequence
data,
such
that
structure-based
comparisons
provide
an
opportunity
to
reveal
viral
'dusk
matter':
sequences
with
low,
but
detectable,
levels
identity
known
available
protein
structures.
Here,
we
present
new
open
computational
resource-RdRp-scan-that
contains
standardized
bioinformatic
toolkit
identify
annotate
data
based
on
detection
RNA-dependent
polymerase
(RdRp)
sequences.
By
combining
RdRp-specific
hidden
Markov
models
(HMMs)
structural
comparisons,
show
RdRp-scan
can
efficiently
detect
RdRp
as
low
10
per
cent
those
not
identifiable
using
standard
sequence-to-sequence
comparisons.
In
addition,
facilitate
placement
newly
detected
virus-like
into
diversity
viruses,
provides
custom
curated
databases
core
motifs,
well
pre-built
multiple
alignments.
parallel,
our
analysis
by
revealed
while
most
taxonomically
unassigned
RdRps
fell
pre-established
clusters,
some
potentially
orders
related
Wolframvirales
Tolivirales.
Finally,
survey
A,
B,
C
motifs
within
database
additional
variations
both
position
might
insights
structure,
function,
evolution
polymerases.
Cell,
Journal Year:
2023,
Volume and Issue:
186(3), P. 646 - 661.e4
Published: Jan. 24, 2023
Viroids
and
viroid-like
covalently
closed
circular
(ccc)
RNAs
are
minimal
replicators
that
typically
encode
no
proteins
hijack
cellular
enzymes
for
replication.
The
extent
diversity
of
agents
poorly
understood.
We
developed
a
computational
pipeline
to
identify
cccRNAs
applied
it
5,131
metatranscriptomes
1,344
plant
transcriptomes.
search
yielded
11,378
spanning
4,409
species-level
clusters,
5-fold
increase
compared
the
previously
identified
elements.
Within
this
diverse
collection,
we
discovered
numerous
putative
viroids,
satellite
RNAs,
retrozymes,
ribozy-like
viruses.
Diverse
ribozyme
combinations
unusual
ribozymes
within
were
identified.
Self-cleaving
in
ambiviruses,
some
mito-like
viruses
capsid-encoding
virus-like
cccRNAs.
broad
presence
transcriptomes
ecosystems
implies
their
host
range
is
far
broader
than
currently
known,
matches
CRISPR
spacers
suggest
replicate
prokaryotes.
BMC Bioinformatics,
Journal Year:
2023,
Volume and Issue:
24(1)
Published: March 26, 2023
Biomedical
researchers
use
alignments
produced
by
BLAST
(Basic
Local
Alignment
Search
Tool)
to
categorize
their
query
sequences.
Producing
such
is
an
essential
bioinformatics
task
that
well
suited
for
the
cloud.
The
cloud
can
perform
many
calculations
quickly
as
store
and
access
large
volumes
of
data.
Bioinformaticians
also
it
collaborate
with
other
researchers,
sharing
results,
datasets
even
pipelines
on
a
common
platform.We
present
ElasticBLAST,
native
application
in
ElasticBLAST
handle
anywhere
from
few
thousands
queries
run
searches
virtual
CPUs
(if
desired),
deleting
resources
when
done.
It
uses
tools
orchestration
request
discounted
instances,
lowering
costs
users.
supported
Amazon
Web
Services
Google
Cloud
Platform.
search
databases
are
user
provided
or
National
Center
Biotechnology
Information.We
show
useful
efficiently
cloud,
demonstrating
two
examples.
At
same
time,
hides
much
complexity
working
threshold
move
work