Extended pairwise local alignment of wild card DNA/RNA sequences using dynamic programming

Abstract

Optimal string alignment is used to discover evolutionary relationships or mutations in DNA/RNA or protein sequences. Errors, missing parts or uncertainty in such a sequence can be covered with wild cards, so-called wild bases. This makes an alignment possible even when the data are corrupted or incomplete. The extended pairwise local alignment of wild card DNA/RNA sequences requires additional calculations in the dynamic programming algorithm and necessitates a subsequent best-and worst-case analysis for the wild card positions. In this paper, we propose an algorithm which solves the problem of input data wild cards, offers a highly flexible set of parameters and displays a detailed alignment output and a compact representation of the mutated positions of the alignment. An implementation of the algorithm can be obtained at https://github.com/sysbio-bioinf/swat+ and http://sysbio.uni-ulm.de/?Software:Swat+.

Unusual accumulation of a wide array of antimicrobial resistance mechanisms in a patient with cytomegalovirus-associated hemophagocytic lymphohistiocytosis: a case report

“…Paired sequence reads were mapped to UL97 and UL54 sequences (Gene ID 3077517 and GenBank accession ABV71585.1, respectively) to obtain corresponding gene sequences from the patient's CMV strain. The sequences were then analyzed by using an online mutational resistance analyzer (MRA) available from the University of Ulm, https://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestler/mra/app/index.php?plugin=form [5]. Ganciclovir resistance was confirmed by the presence of the A594V mutation in UL97 [6] What was unique in our patient compared to other reported CMV-associated HLH cases was the overwhelming infection with MDROs.…”