ProPIP: a tool for progressive multiple sequence alignment with Poisson Indel Process

Background Current alignment tools typically lack an explicit model of indel evolution, leading to artificially short inferred alignments (i.e., over-alignment) due to inconsistencies between the indel history and the phylogeny relating the input sequences. Results We present a new progressive multiple sequence alignment tool ProPIP. The process of insertions and deletions is described using an explicit evolutionary model—the Poisson Indel Process or PIP. The method is based on dynamic programming and is implemented in a frequentist framework. The source code can be compiled on Linux, macOS and Microsoft Windows platforms. The algorithm is implemented in C++ as standalone program. The source code is freely available on GitHub at https://github.com/acg-team/ProPIP and is distributed under the terms of the GNU GPL v3 license. Conclusions The use of an explicit indel evolution model allows to avoid over-alignment, to infer gaps in a phylogenetically consistent way and to make inferences about the rates of insertions and deletions. Instead of the arbitrary gap penalties, the parameters used by ProPIP are the insertion and deletion rates, which have biological interpretation and are contextualized in a probabilistic environment. As a result, indel rate settings may be optimised in order to infer phylogenetically meaningful gap patterns.

ViralMSA: Massively scalable reference-guided multiple sequence alignment of viral genomes

MotivationIn molecular epidemiology, the identification of clusters of transmissions typically requires the alignment of viral genomic sequence data. However, existing methods of multiple sequence alignment scale poorly with respect to the number of sequences.ResultsViralMSA is a user-friendly reference-guided multiple sequence alignment tool that leverages the algorithmic techniques of read mappers to enable the multiple sequence alignment of ultra-large viral genome datasets. It scales linearly with the number of sequences, and it is able to align tens of thousands of full viral genomes in seconds.AvailabilityViralMSA is freely available at https://github.com/niemasd/ViralMSA as an open-source software [email protected]

CUDA-Parttree: A Multiple Sequence Alignment Parallel Strategy in GPU

In this paper, we propose and evaluate CUDA-Parttree, a parallel strategy that executes the first phase of the MAFFT Parttree Multiple Sequence Alignment tool (distance matrix calculation with 6mers) on GPU. When compared to Parttree, CUDA-Parttree obtained a speedup of 6.10x on the distance matrix calculation for the Cyclodex gly tran (50, 280 sequences) set, reducing the execution time from 33.94s to 5.57s. Including data conversion and movement to/from the GPU, the speedup was 2.59x. With the sequence set Syn 100000 (100, 000 sequences), a speedup of 4.46x was attained, reducing execution time from 209.54s to 47.00s.

Prediction of Four Novel SNPs V17M, R11H, A66T, and F57S in the SBDS Gene Possibly Associated with Formation of Shwachman-Diamond Syndrome, using an Insilico Approach

Shwachman-Diamond syndrome SDS (MIM 260400) is an autosomal recessive disorder. Characterized by exocrine insufficiency of the pancreas, bone marrow hypoplasia resulting in cytopenias, especially neutropenia, variable degree of skeletal abnormalities, failure to thrive, and increasing risk of developing myelodysplasia or transformation to leukemia. SDS is mainly caused by Shwachman Bodian Diamond Syndrome gene (MIM ID 607444). SBDS gene is 14899 bp in length, located in chromosome seven in the eleventh region of the long arm, and is composed of five exons. It's a ribosomal maturation factor which encodes a highly conservative protein that has widely unknown functions despite of its abundance in the nucleolus. A total number of 53 SNPs of homo sapiens SBDS gene were obtained from the national center for biotechnology information (NCBI) analyzed using translational tools, 7 of which were deleterious according to SIFT server and were further analyzed using several softwares (Polyhen-2, SNPs&Go, I-Mutant 2.0, Mutpred2, structural analysis soft wares and multiple sequence alignment tool). Four SNPs (rs11557408 (V17M), rs11557409 (R11H), rs367842164 (A66T), and rs376960114 (F57S)) were predicted to be disease causing, localized at highly conservative regions of the SBDS protein and were not reported in any previous study. In addition, the study predicts new functions of the SBDS protein DNA related, and suggests explanations for Patients developing cytopenias and failure to thrive through genetic coexpression and physical interaction with RBF1 and EXOSC3, respectively.

Constrained Multiple Sequence Alignment Tool Development and Its Application to RNase Family Alignment

In this paper, we design a heuristic algorithm of computing a constrained multiple sequence alignment (CMSA for short) for guaranteeing that the generated alignment satisfies the user-specified constraints that some particular residues should be aligned together. If the number of residues needed to be aligned together is a constant α, then the time-complexity of our CMSA algorithm for aligning K sequences is O(αKn4), where n is the maximum of the lengths of sequences. In addition, we have built up such a CMSA software system and made several experiments on the RNase sequences, which mainly function in catalyzing the degradation of RNA molecules. The resulting alignments illustrate the practicability of our method.