Track of fruitfly
polytracts
Description
This tract displays
polytracts in the fruitfly reference
genome. A polytract is defined as a tract of tandem mono-nucleotide,
di-nucleotide, or tri-nucleotide repeats, termed MNR, DNR, and TNR,
respectively. Each MNR and DNR span at least six units, and each TNR spans at
least three units. Incomplete terminal motif is included in a polytract (so
that the length of a DNR or TNR is not necessarily multiple of 2 or 3).
Display Conventions and Configuration
Four shades of grayness are used to distinguish four classes
of data, including three clades of polytracts (MNR, DNR, and TNR) and the
polytract hinge.
- -
Mono-Nucleotide Repeat (MNR)
- - Di-Nucleotide Repeat (DNR)
- - Tri-Nucleotide Repeat (TNR)
- - polytract break-point (hinge)
Methods
A polytract is defined as a tract
of mono-nucleotide, di-nucleotide, or tri-nucleotide tandemly repeated motifs,
with possibly incomplete terminal motif included, where the minimum number of
repeated units are 6 for MNR and 3 for DNR and TNR. Polytracts were identified
through a string matching between a pattern and each chromosome sequence, with
assistance from R packages ¡°stringr¡± (https://CRAN.R-project.org/package=stringr)
and ¡°BSgenome.Dmelanogaster.UCSC.dm6¡± (www.bioconductor.org; DOI: 10.18129/B9.bioc.BSgenome).
Accommodating the complementarity between a purine and pyrimidine pair (A:T and
G:C), MNRs comprise A/T and G/C species, DNRs comprise TA, CT/GA,
CA/GT, and GC species, and TNRs comprise AAC,
AAG, AAT, ACC, GAC, ACT, CAG, AGG, ATC, and CGG species. That is, our resultant polytract dataset consisted of
two types of MNRs, four types of DNRs, and ten types of TNRs.
Credits
Data were generated and processed in Guo Bioinformatics Lab
at UNM Comprehensive Cancer Center. For inquiries, please contact Dr. Hui Yu
(huiyu1@salud.unm.edu).
References
Yu H, Zhao S, Ness S, Kang H, Sheng Q, Samuels DC, Oyebamiji
O, Guo Y. Non-canonical RNA-DNA differences and other
human genomic features are associated with very short tandem repeats. PLoS Comp Biol. 2020 In
revision.