Genomic Scaffold Filling: A Progress Report

Bioinformatics Research and Applications

Liu

Zhong

et al. 2016

Self Cite

In mass spectrometry-based de novo protein sequencing, it is hard to complete the sequence of the whole protein. Motivated by this we study the (one-sided) problem of filling a protein scaffold with some missing amino acids, given a sequence of contigs none of which is allowed to be altered, with respect to a complete reference protein of length n, such that the BLOSUM62 score between and the filled sequence is maximized. We show that this problem is polynomial-time solvable in O(n 26 ) time. We also consider the case when the contigs are not of high quality and they are concatenated into an (incomplete) sequence , where the missing amino acids can be inserted anywhere in to obtain , such that the BLOSUM62 score between and is maximized. We show that this problem is polynomial-time solvable in O(n 22 ) time. Due to the high time complexity, both of these algorithms are impractical, we hence present several algorithms based on greedy and local search, trying to solve the problems practically. The empirical results, based on some antibody and mammalian proteins, show that the algorithms can fill protein scaffolds with high quality, provided that a good pair of scaffold and reference are given.

Section: Introductionsupporting

confidence: 61%

Section: Introductionmentioning

confidence: 99%

Filling a Protein Scaffold with a Reference

Bioinformatics Research and Applications

Liu

Zhong

et al. 2016

Self Cite

Section: Introductionsupporting

confidence: 54%

“…For protein sequences, the order of its amino acids is probably even more critical compared with genomes. Given a complete genome

scriptG

and a genomic scaffold ℋ, the one-sided scaffold filling problem, i.e., filling ℋ into ℋ′ such that the number of adjacencies between

scriptG

and ℋ′ is maximized, is NP-hard [8], [9] and constant-factor approximation algorithms are known [10], [19]. …”

Section: Introductionmentioning

confidence: 99%

Filling a Protein Scaffold With a Reference

IEEE Trans.on Nanobioscience

Liu

Zhong

et al. 2017

Self Cite

In mass spectrometry-based de novo protein sequencing, it is hard to complete the sequence of the whole protein. Motivated by this we study the (one-sided) problem of filling a protein scaffold scriptS with some missing amino acids, given a sequence of contigs none of which is allowed to be altered, with respect to a complete reference protein scriptP of length n, such that the BLOSUM62 score between scriptP and the filled sequence S′ is maximized. We show that this problem is polynomial-time solvable in O(n26) time. We also consider the case when the contigs are not of high quality and they are concatenated into an (incomplete) sequence scriptI, where the missing amino acids can be inserted anywhere in scriptI to obtain scriptI′, such that the BLOSUM62 score between scriptP and scriptI′ is maximized. We show that this problem is polynomial-time solvable in O(n22) time. Due to the high time complexity, both of these algorithms are impractical, we hence present several algorithms based on greedy and local search, trying to solve the problems practically. The empirical results, based on some antibody and mammalian proteins, show that the algorithms can fill protein scaffolds with high quality, provided that a good pair of scaffold and reference are given.

“…(In fact, all other research on scaffold filling simply used an incomplete sequence as a scaffold.) For a recent survey on the genomic scaffold filling research, the readers are referred to 28 .…”

Section: Introductionmentioning

confidence: 99%

A 2-approximation algorithm for the contig-based genomic scaffold filling problem

Jiang

J. Bioinform. Comput. Biol.

Zhu

et al. 2018

Self Cite

The genomic scaffold filling problem has attracted a lot of attention recently. The problem is on filling an incomplete sequence (scaffold) [Formula: see text] into [Formula: see text], with respect to a complete reference genome [Formula: see text], such that the number of common/shared adjacencies between [Formula: see text] and [Formula: see text] is maximized. The problem is NP-complete, and admits a constant-factor approximation. However, the sequence input [Formula: see text] is not quite practical and does not fit most of the real datasets (where a scaffold is more often given as a list of contigs). In this paper, we revisit the genomic scaffold filling problem by considering this important case when a scaffold [Formula: see text] is given, the missing genes can only be inserted in between the contigs, and the objective is to maximize the number of common adjacencies between [Formula: see text] and the filled genome [Formula: see text]. For this problem, we present a simple NP-completeness proof, we then present a factor-2 approximation algorithm.