The Power of Alignment-Free Histogram-based Functions: a Comprehensive Genome Scale Experimental Analysis – Version 1

06/27/2021
by   Giuseppe Cattaneo, et al.
0

Motivation: Alignment-free (AF, for short) distance/similarity functions are a key tool for sequence analysis. Experimental studies on real datasets abound and, to some extent, there are also studies regarding their control of false positive rate (Type I error). However, assessment of their power, i.e., their ability to identify true similarity, has been limited to some members or variants of the family and the asymptotic theoretic results have been complemented by experimental studies on short sequences, not adequate for current genome-scale applications. Such a State of the Art is methodologically problematic, since information regarding a key feature such as power is either missing or limited. Results: By concentrating on histogram-based AF functions, we perform the first coherent and uniform evaluation of the power of those functions, involving also Type I error for completeness. The experiments carried out are extensive, as we use two Alternative models of important genomic features (CIS Regulatory Modules and Horizontal Gene Transfer), sequence lengths from a few thousand to millions and different values of k. As a result, and using power, we provide a characterization of those AF functions that is novel and informative. Indeed, we identify weak and strong points of each function considered, which may be used as a guide to choose one for analysis tasks. In synthesis, and quite remarkably, of the fifteen functions that we have considered, only four stand out. Finally, in order to encourage the use of our methodology for validation of future AF functions, the Big Data platform supporting it is public.

READ FULL TEXT

page 7

page 8

research
05/02/2020

An Extensible, Scalable Spark Platform for Alignment-free Genomic Analysis – Version 1

Alignment-free similarity/distance functions, a computationally convenie...
research
05/02/2020

An Extensible, Scalable Spark Platform for Alignment-free Genomic Analysis – Version 2

Motivation: Alignment-free distance and similarity functions (AF functio...
research
01/17/2019

BioSEAL: In-Memory Biological Sequence Alignment Accelerator for Large-Scale Genomic Data

Genome sequences contain hundreds of millions of DNA base pairs. Finding...
research
02/12/2019

PLIT: An alignment-free computational tool for identification of long non-coding RNAs in plant transcriptomic datasets

Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs which play...
research
06/10/2019

Big Variates: Visualizing and identifying key variables in a multivariate world

Big Data involves both a large number of events but also many variables....
research
10/11/2019

Statistical Linear Models in Virus Genomic Alignment-free Classification: Application to Hepatitis C Viruses

Viral sequence classification is an important task in pathogen detection...

Please sign up or login with your details

Forgot password? Click here to reset