PMID- 37335492
OWN - NLM
STAT- MEDLINE
DCOM- 20230621
LR  - 20230622
IS  - 1940-6029 (Electronic)
IS  - 1064-3745 (Linking)
VI  - 2672
DP  - 2023
TI  - Visualization of Oligonucleotide-Based Probes Along Pseudochromosomes Using 
      RIdeogram, KaryoploteR, and Circlize (Circos).
PG  - 409-444
LID - 10.1007/978-1-0716-3226-0_26 [doi]
AB  - Fluorescence in situ hybridization (FISH) using oligonucleotide-based probes is 
      an innovative modification of classic FISH techniques, enabling karyotypic 
      identifications. Here, we exemplarily describe the design and in silico 
      visualization of oligonucleotide-based probes derived from the Cucumis sativus 
      genome. Additionally, the probes are also plotted comparatively to the closely 
      related Cucumis melo genome. The visualization process is realized in R using 
      various libraries for linear or circular plots including RIdeogram, KaryoploteR, 
      and Circlize.
CI  - (c) 2023. The Author(s), under exclusive license to Springer Science+Business 
      Media, LLC, part of Springer Nature.
FAU - Mann, Ludwig
AU  - Mann L
AD  - Faculty of Biology, Technische Universitat Dresden, Dresden, Germany. 
      Ludwig.Mann@tu-dresden.de.
FAU - Maiwald, Sophie
AU  - Maiwald S
AD  - Faculty of Biology, Technische Universitat Dresden, Dresden, Germany.
LA  - eng
PT  - Journal Article
PL  - United States
TA  - Methods Mol Biol
JT  - Methods in molecular biology (Clifton, N.J.)
JID - 9214969
RN  - 0 (Oligonucleotide Probes)
RN  - 0 (Oligonucleotides)
SB  - IM
MH  - In Situ Hybridization, Fluorescence
MH  - Oligonucleotide Probes/genetics
MH  - *Genome
MH  - *Cucumis sativus/genetics
MH  - Oligonucleotides/genetics
OTO - NOTNLM
OT  - Comparative genomics
OT  - FISH
OT  - Hybrid genomes
OT  - Oligo-FISH
OT  - Phylogenomics
OT  - R
OT  - Visualization
EDAT- 2023/06/19 13:08
MHDA- 2023/06/21 06:42
CRDT- 2023/06/19 11:10
PHST- 2023/06/21 06:42 [medline]
PHST- 2023/06/19 13:08 [pubmed]
PHST- 2023/06/19 11:10 [entrez]
AID - 10.1007/978-1-0716-3226-0_26 [doi]
PST - ppublish
SO  - Methods Mol Biol. 2023;2672:409-444. doi: 10.1007/978-1-0716-3226-0_26.