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We introduce the notion of Levenshtein graphs, an analog to Hamming graphs but using the edit distance instead of the Hamming distance; in particular, vertices in Levenshtein graphs may be strings (i.e., words or sequences of characters in a reference alphabet) of possibly different lengths. We study various properties of these graphs, including a necessary and sufficient condition for their shortest path distance to be identical to the edit distance, and characterize their automorphism group and determining number. We also bound the metric dimension (i.e. minimum resolving set size) of Levenshtein graphs. Regarding the latter, recall that a run is a string composed of identical characters. We construct a resolving set of two-run strings and an algorithm that computes the edit distance between a string of length k and any single-run or two-run string in operations.
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The effect of genome graph expressiveness on the discrepancy between genome graph distance and string set distance
Motivation: Intra-sample heterogeneity describes the phenomenon where a genomic sample contains a diverse set of genomic sequences. In practice, the true string sets in a sample are often unknown due to limitations in sequencing technology. In order to compare heterogeneous samples, genome graphs can be used to represent such sets of strings. However, a genome graph is generally able to represent a string set universe that contains multiple sets of strings in addition to the true string set. This difference between genome graphs and string sets is not well characterized. As a result, a distance metric between genome graphs may not match the distance between true string sets. Results: We extend a genome graph distance metric, Graph Traversal Edit Distance (GTED) proposed by Ebrahimpour Boroojeny et al., to FGTED to model the distance between heterogeneous string sets and show that GTED and FGTED always underestimate the Earth Mover’s Edit Distance (EMED) between string sets. We introduce the notion of string set universe diameter of a genome graph. Using the diameter, we are able to upper-bound the deviation of FGTED from EMED and to improve FGTED so that it reduces the average error in empirically estimating the similarity between true string sets. On simulated T-cell receptor sequences and actual Hepatitis B virus genomes, we show that the diameter-corrected FGTED reduces the average deviation of the estimated distance from the true string set distances by more than 250%. Availability and implementation: Data and source code for reproducing the experiments are available at: https:// github.com/Kingsford-Group/gtedemedtest/.
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- Award ID(s):
- 1937540
- PAR ID:
- 10328101
- Date Published:
- Journal Name:
- ISCB ISMB 2022
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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