A Survey of K-mer Methods and Applications in Bioinformatics
Computational and Structural Biotechnology Journal,
Год журнала:
2024,
Номер
23, С. 2289 - 2303
Опубликована: Май 21, 2024
The
rapid
progression
of
genomics
and
proteomics
has
been
driven
by
the
advent
advanced
sequencing
technologies,
large,
diverse,
readily
available
omics
datasets,
evolution
computational
data
processing
capabilities.
vast
amount
generated
these
advancements
necessitates
efficient
algorithms
to
extract
meaningful
information.
K-mers
serve
as
a
valuable
tool
when
working
with
large
offering
several
advantages
in
speed
memory
efficiency
carrying
potential
for
intrinsic
biological
functionality.
This
review
provides
an
overview
methods,
applications,
significance
k-mers
genomic
proteomic
analyses,
well
utility
absent
sequences,
including
nullomers
nullpeptides,
disease
detection,
vaccine
development,
therapeutics,
forensic
science.
Therefore,
highlights
pivotal
role
addressing
current
problems
underscores
their
future
breakthroughs
research.
Язык: Английский
Unraveling diversity by isolating peptide sequences specific to distinct taxonomic groups
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2025,
Номер
unknown
Опубликована: Фев. 8, 2025
Abstract
The
identification
of
succinct,
universal
fingerprints
that
enable
the
characterization
individual
taxonomies
can
reveal
insights
into
trait
development
and
have
widespread
applications
in
pathogen
diagnostics,
human
healthcare,
ecology
biomes.
Here,
we
investigated
existence
peptide
k-mer
sequences
are
exclusively
present
a
specific
taxonomy
absent
every
other
taxonomic
level,
termed
quasi-primes.
By
analyzing
proteomes
across
24,073
species,
identified
quasi-prime
peptides
to
superkingdoms,
kingdoms,
phyla,
uncovering
their
distributions
functional
relevance.
These
exhibit
remarkable
sequence
uniqueness
at
six-
seven-amino-
acid
lengths,
offering
evolutionary
divergence
lineage-specific
adaptations.
Moreover,
show
loci
more
prone
harboring
pathogenic
variants,
underscoring
significance.
This
study
introduces
quasi-primes
offers
contributions
proteomic
diversity,
pathways,
adaptations
tree
life,
while
emphasizing
potential
impact
on
health
disease.
Язык: Английский