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A comparison of 10 most popular Multiple Sequence Alignment (MSA) tools, namely, MUSCLE, MAFFT(L-INS-i), MAFFT (FFT-NS-2), T-Coffee, ProbCons, SATe, Clustal Omega, Kalign, Multalin, and Dialign-TX is presented. We also focused on the significance of some implementations embedded in algorithm of each tool. Based on 10 simulated trees of different number of taxa generated by R, 400 known alignments and sequence files were constructed using indel-Seq-Gen. A total of 4000 test alignments were generated to study the effect of sequence length, indel size, deletion rate, and insertion rate. Results showed that alignment quality was highly dependent on the number of deletions and insertions in the sequences and that the sequence length and indel size had a weaker effect. Overall, ProbCons was consistently on the top of list of the evaluated MSA tools. SATe, being little less accurate, was 529.10% faster than ProbCons and 236.72% faster than MAFFT(L-INS-i). Among other tools, Kalign and MUSCLE achieved the highest sum of pairs. We also considered BALiBASE benchmark datasets and the results relative to BAliBASE- and indel-Seq-Gen-generated alignments were consistent in the most cases.

The 3-D flow of Casson nanofluid over a stretched sheet with chemical reactions, velocity slip, thermal radiation, and Brownian motion have been analyzed. By employing the similarity transformation, the ODE are obtained from the fluidic system PDE. The transformed ODE are handled for the numerical solution of the proposed fluidic problem by incorporating shooting technique. To compare the obtained numerical results, Lobatto 111A method has been implemented, with 5-8 decimal places of accuracy. The numerical data for the fluidic parameters of interest are demonstrated in the tabular form, further few proficient parameters effects like magnetic parameter, Lewis number, stretching rate parameter, the thermal radiation parameter and Prandtl number on velocity, temperature and concentration profiles have been exhibited numerically as well as graphically. By enhancing the velocity slip parameter, increment is examined in temperature and concentration profiles while opposite behavior is recorded in the velocity profile. Both the concentration and temperature profiles decline with the increase in the Stretching rate ratio parameter.

Background:Current advancements in next-generation sequencing technology have made possible to sequence whole genome but assembling a large number of short sequence reads is still a big challenge. In this article, we present the comparative study of seven assemblers, namely, ABySS, Velvet, Edena, SGA, Ray, SSAKE, and Perga, using prokaryotic and eukaryotic paired-end as well as single-end data sets from Illumina platform.Results:Results showed that in case of single-end data sets, Velvet and ABySS outperformed in all the seven assemblers with comparatively low assembling time and high genome fraction. Velvet consumed the least amount of memory than any other assembler. In case of paired-end data sets, Velvet consumed least amount of time and produced high genome fraction after ABySS and Ray. In terms of low memory usage, SGA and Edena outperformed in all the assemblers. Ray also showed good genome fraction; however, extremely high assembling time consumed by the Ray might make it prohibitively slow on larger data sets of single and paired-end data.Conclusions:Our comparison study will provide assistance to the scientists for selecting the suitable assembler according to their data sets and will also assist the developers to upgrade or develop a new assembler for de novo assembling.

In this study, the competency of numerical computational framework based on Lobatto IIIA technique is utilized for dynamical analysis of the Darcy-Forchheimer flow of Sisko nanomaterial with nonlinear thermal radiation. The resultant PDEs of the Sisko fluid model expressions are transformed into system of nonlinear ODEs by exploiting the similarity variables. Graphical representations and numerical illustrations are used to envisage the characteristics of various physical parameters of interest on velocity profile, nanoparticles concentration, and temperature distribution of Sisko fluidic system. In addition, skin friction and Nusselt number are numerically examined with observation that the material parameter of Sisko fluid increases the velocity profile as well as Nusselt number while decreasing temperature, concentration profiles, and skin friction coefficient.

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