CSBL::Computational & Synthetic Biology Laboratory at
Genome analysis begins with annotation.
- Precise and accurate annotation is essential for genomic,
transcriptomic, functional analysis. We developed a light-weight
portable annotation pipeline that can be maintained by small-scale
individual laboratory.
FunGap (Fungal Genome Annotation Pipeline)
- GitHub Download
- FunGAP performs gene prediction on given genome assembly and RNA-seq
reads. At the moment, RNA-seq data is mandatory for gene
prediction.
- Citation: “FunGAP: Fungal Genome Annotation Pipeline using
evidence-based gene model evaluation”. In: BIOINFORMATICS (OXFORD,
ENGLAND) 33.18 (2017), pp. 2936-2937. DOI: 10.1093/bioinformatics/btx353.
PMID: 28582481
p-CAPS (prokaryotic-Contig Annotation Pipeline Server)
- GitHub Download
- p-CAPS is a portable web server that can annotate any chunk of DNA
assembly from contigs to scaffolds to genome.
- Citation: “Prokaryotic Contig Annotation Pipeline Server: Web
Application for a Prokaryotic Genome Annotation Pipeline Based on the
Shiny App Package”. In: JOURNAL OF COMPUTATIONAL BIOLOGY : A JOURNAL OF
COMPUTATIONAL MOLECULAR CELL BIOLOGY 24.9 (2017), pp. 917-922. DOI: 10.1089/cmb.2017.0066.
PMID: 28632399
pyGCAP: a python Gene
Cluster Annotation &
Profiling
- Github Download
- pyGCAP is a python package for Probe-based Gene Cluster Finding in
Large Microbial Genome Database. It is developed as a URAP
(undergraduate research apprentice project) during 2023-2024 Winter by
Jisu. The manuscript is prepared
for submitting a peer-reviewed journal.
pyCDM4F: a python Chill
Day Model for
Flowering date
- Github
- pyCDM4F is a python package for predicting cherry blooming/flowering
date based on the Chill-Day Model. Model prediction accuracy for Korean
local areas is best among those previously published models. It is
developed as a URAP (undergraduate research apprentice project) during
2024 Summer by Songwon. It will open soon (check this
page out later!)