EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements

BMC Bioinformatics
Tom HartmannMartin Middendorf

Abstract

To study the differences between two unichromosomal circular genomes, e.g., mitochondrial genomes, under the tandem duplication random loss (TDRL) rearrangement it is important to consider the whole set of potential TDRL rearrangement events that could have taken place. The reason is that for two given circular gene orders there can exist different TDRL rearrangements that transform one of the gene orders into the other. Hence, a TDRL event cannot always be reconstructed only from the knowledge of the circular gene order before a TDRL event and the circular gene order after it. We present the program EqualTDRL that computes and illustrates the complete set of TDRLs for pairs of circular gene orders that differ by only one TDRL. EqualTDRL considers the circularity of the given genomes and certain restrictions on the TDRL rearrangements. Examples for the latter are sequences of genes that have to be conserved during a TDRL or pairs of genes that frame intergenic regions which might represent remnants of duplicated genes. Additionally, EqualTDRL allows to determine the set of TDRLs that are minimum with respect to the number of duplicated genes. EqualTDRL supports scientists to study the complete set of TDRLs that possibly could h...Continue Reading

References

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Jul 12, 2018·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Tom HartmannMartin Middendorf

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Datasets Mentioned

BETA
MG255141.1
MG255136.1

Software Mentioned

CMalign
TDRL
ggplot2
HMMsearch
BLAST
Infernal
CREx2
EqualTDRL
HMMalign
R

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