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Software & Database
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MECAT
We present a tool that combines fast
mapping, error correction, and de
novo assembly (MECAT) for processing
single-molecule sequencing (SMS)
reads. MECAT’s computing efficiency
is superior to that of current
tools, while the results MECAT
produces are comparable or improved.
MECAT enables reference mapping or
de novo assembly of large genomes
using SMS reads on a single
computer.
Source Code: https://github.com/xiaochuanle/MECAT |
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MethSMRT
DNA methylation is an important type
of epigenetic modifications, where
5- methylcytosine (5mC),
6-methyadenine (6mA) and
4-methylcytosine (4mC) are the most
common types. Previous efforts have
been largely focused on 5mC,
providing invaluable insights into
epigenetic regulation through DNA
methylation. Recently developed
single-molecule real-time (SMRT)
sequencing technology provides a
unique opportunity to detect the
less studied DNA 6mA and 4mC
modifications at single-nucleotide
resolution. With a rapidly increased
amount of SMRT sequencing data
generated, there is an emerging
demand to systematically explore DNA
6mA and 4mC modifications from these
data sets. MethSMRT is the first
resource hosting DNA 6mA and 4mC
methylomes. All the data sets were
processed using the
same analysis pipeline with the same
quality control. The current version
of the database provides a platform
to store, browse, search and
download epigenome-wide methylation
profiles of 156 species, including
seven eukaryotes such as
Arabidopsis, C. elegans, Drosophila,
mouse and yeast, as well as 149
prokaryotes. It also offers a genome
browser to visualize the methylation
sites and related information
such as single nucleotide
polymorphisms (SNP) and genomic
annotation. Furthermore, the
database provides a quick summary of
statistics of methylome of 6mA and
4mC and predicted methylation motifs
for each species.
Website:
http://sysbio.sysu.edu.cn/methsmrt/
http://sysbio.gzzoc.com/methsmrt/
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RPFdb
Translational control is crucial in
the regulation of gene expression
and deregulation of translation is
associated with a wide range of
cancers and human diseases. Ribosome
profiling is a technique that
provides genome wide information of
mRNA in translation based on deep
sequencing of ribosome protected
mRNA fragments (RPF). RPFdb is a
comprehensive resource for hosting,
analyzing and visualizing RPF data.
The current version of database
contains 777 samples from 82 studies
in 8 species, processed and
reanalyzed by a unified pipeline.
There are two ways to query the
database: by keywords of studies or
by genes. The outputs are presented
in three levels. (I) Study level:
including meta information of
studies and reprocessed data for
gene expression of translated mRNAs;
(II) Sample level: including global
perspective of translated mRNA and a
list of the most translated mRNA of
each sample from a study; (III) Gene
level: including normalized sequence
counts of translated mRNA on
different genomic location of a gene
from multiple samples and studies.
To explore rich information provided
by RPF, RPFdb also provides a genome
browser to query and visualize
context-specific translated mRNA.
Overall the database provides a
simple way to search, analyze,
compare, visualize and download RPF
data sets.
Website:
http://www.rpfdb.org
http://sysbio.sysu.edu.cn/rpfdb/
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