NAR Genomics and Bioinformatics,
Год журнала:
2024,
Номер
6(4)
Опубликована: Сен. 28, 2024
Abstract
Taxonomic
classification
of
viruses
is
essential
for
understanding
their
evolution.
Genomic
at
higher
taxonomic
ranks,
such
as
order
or
phylum,
typically
based
on
alignment
and
comparison
amino
acid
sequence
motifs
in
conserved
genes.
Classification
lower
genus
species,
usually
nucleotide
identities
between
genomic
sequences.
Building
our
whole-genome
analytical
framework,
we
here
describe
Genome
Relationships
Applied
to
Viral
Taxonomy
Version
2
(GRAViTy-V2),
which
encompasses
a
greatly
expanded
range
features
numerous
optimisations,
packaged
an
application
that
may
be
used
general-purpose
virus
tool.
Using
28
datasets
derived
from
the
ICTV
2022
taxonomy
proposals,
GRAViTy-V2
output
was
compared
against
human
expert-curated
classifications
assignments
2023
round
changes.
produced
taxonomies
equivalent
manually-curated
versions
down
family
level
almost
all
cases,
species
levels.
The
majority
discrepant
results
arose
errors
coding
annotations
INDSC
records,
inclusion
incomplete
genome
sequences
analysis.
Analysis
times
ranged
1-506
min
(median
3.59)
with
17-1004
genomes
mean
length
3000–1
000
bases.
Bacterial
small
regulatory
RNA
(sRNA)
plays
a
crucial
role
in
cell
metabolism
and
could
be
used
as
new
potential
drug
target
the
treatment
of
pathogen-induced
disease.
However,
experimental
methods
for
identifying
sRNAs
still
require
large
investment
human
material
resources.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Ноя. 14, 2024
Abstract
Motivation
Generating
phylogenetic
trees
from
genomic
data
is
essential
in
understanding
biological
systems.
Each
step
of
this
complex
process
has
received
extensive
attention
the
literature,
and
been
significantly
streamlined
over
years.
Given
volume
publicly
available
genetic
data,
obtaining
genomes
for
a
wide
selection
known
species
straightforward.
However,
analyzing
that
same
order
to
generate
tree
multi-step
with
legitimate
scientific
technical
challenges,
often
requires
significant
input
domain-area
scientist.
Results
We
present
Poplar,
new,
computational
pipeline,
address
logistical
issues
arise
when
constructing
trees.
It
provides
framework
runs
state-of-the-art
software
steps
beginning
genome
or
without
an
annotation,
resulting
tree.
Running
Poplar
no
external
databases.
In
execution,
it
enables
parallelism
execution
clusters
cloud
computing.
The
generated
by
match
closely
published
usage
performance
far
simpler
quicker
than
manually
running
pipeline.
Availability
Implementation
Freely
on
GitHub
at
https://github.com/sandialabs/poplar
.
Implemented
using
Python
supported
Linux.
Supplementary
Information
Newick
versions
reference
Scientific Reports,
Год журнала:
2024,
Номер
14(1)
Опубликована: Окт. 23, 2024
Preoperative
identification
of
causal
organism(s)
is
crucial
for
effective
prosthetic
joint
infection
treatment.
Herein,
we
explore
the
clinical
application
a
novel
metatranscriptomic
(MT)
workflow,
CSI-Dx,
to
detect
pathogens
associated
with
infection.
MT
provides
insight
into
transcriptionally
active
microbes,
overcoming
limitations
culture-based
and
available
molecular
methods.
This
study
included
340
human
synovial
fluid
specimens
subjected
CSI-Dx
traditional
Exploratory
analyses
were
conducted
determine
sensitivity
specificity
detecting
clinically-relevant
taxa.
Our
findings
provide
insights
microbial
community
composition
from
arthroplasty
patients
demonstrate
potential
utility
aiding
diagnosis.
approach
offers
improved
acceptable
compared
culture,
enabling
detection
culturable
non-culturable
microorganisms.
Furthermore,
valuable
information
on
antimicrobial
resistance
gene
expression.
While
further
optimization
needed,
integrating
technologies
like
routine
practice
can
revolutionize
diagnosis
by
offering
comprehensive
snapshot
pathogens.
NAR Genomics and Bioinformatics,
Год журнала:
2024,
Номер
6(4)
Опубликована: Сен. 28, 2024
Abstract
Taxonomic
classification
of
viruses
is
essential
for
understanding
their
evolution.
Genomic
at
higher
taxonomic
ranks,
such
as
order
or
phylum,
typically
based
on
alignment
and
comparison
amino
acid
sequence
motifs
in
conserved
genes.
Classification
lower
genus
species,
usually
nucleotide
identities
between
genomic
sequences.
Building
our
whole-genome
analytical
framework,
we
here
describe
Genome
Relationships
Applied
to
Viral
Taxonomy
Version
2
(GRAViTy-V2),
which
encompasses
a
greatly
expanded
range
features
numerous
optimisations,
packaged
an
application
that
may
be
used
general-purpose
virus
tool.
Using
28
datasets
derived
from
the
ICTV
2022
taxonomy
proposals,
GRAViTy-V2
output
was
compared
against
human
expert-curated
classifications
assignments
2023
round
changes.
produced
taxonomies
equivalent
manually-curated
versions
down
family
level
almost
all
cases,
species
levels.
The
majority
discrepant
results
arose
errors
coding
annotations
INDSC
records,
inclusion
incomplete
genome
sequences
analysis.
Analysis
times
ranged
1-506
min
(median
3.59)
with
17-1004
genomes
mean
length
3000–1
000
bases.
