Alignment Software Research Articles

Molecular approach to the characterization of lipase encoding genes from Moraxella sp. SBE01

Lipase from Moraxella sp. SBE01 is an expression of the gene encoding lipase. Detection and characterization of the Moraxella sp. SBE01 lipase coding gene is necessary for large-scale lipase production through genetic engineering. This study aimed to observe the molecular weight, amino acid sequence, length, and conserved amino acids in the DNA encoding the lipase gene, with the goal of identifying and characterizing the lipase-coding gene from Moraxella sp. SBE01. The primer design process was conducted to amplify the lipase gene from Moraxella sp. SBE01 using specialized software for sequence alignment and phylogenetic analysis. Amplification was carried out using PCR with the designed primer, forward primer (GTC ATG ATG TAC TTC CAY GGN GGN GG), reverse primer (GGT TGC CGC CGG CDS WRT CNC C). PCR was carried out under pre-denatured conditions at 95°C (3 minutes), followed by 30 cycles of denaturation at 95°C, annealing at 66°C (30 seconds), 70°C elongations (1 minute) and final elongation of 70°C (10 minutes). The PCR results were electrophoresed using 1% agarose gel with a 1 kb DNA marker. The PCR results were sequenced and analyzed for gene and amino acid sequences and the type of lipase expressed. Sequencing resulted in 387 bp of the nucleotide sequence. The gene and amino acid sequences from Moraxella sp. SBE01 had high homology with the gene and amino acid sequences from Moraxella sp. strain TA144. The lipase gene encodes a protein consisting of 129 amino acids and contains a conserved HGG (His-Gly-Gly) motif, which is characteristic of lipases in family IV, also known as the hormone-sensitive lipase (HSL) family. This conserved sequence suggests that the lipase shares structural and functional similarities with other enzymes in the HSL family, playing a key role in lipid metabolism.

Markerauto2: A fast and robust fully automatic fiducial marker-based tilt series alignment software for electron tomography

Cryoelectron tomography (cryo-ET) has become an indispensable technology for visualizing in situ biological ultrastructures, where the tilt series alignment is the key step to obtain a high-resolution three-dimensional reconstruction. Specifically, with the advent of high-throughput cryo-ET data collection, there is an increasing demand for high-accuracy and fully automatic tilt series alignment, to enable efficient data processing. Here, we propose Markerauto2, a fast and robust fully automatic software that enables accurate fiducial marker-based tilt series alignment. Markerauto2 implements the following novel pipelines: (1) an accelerated high-precision fiducial marker detection with wavelet multiscale template, (2) an ultra-fast and robust fiducial marker tracking supported by hashed geometric features, (3) a high-angle fiducial marker supplementation strategy to produce more complete tracks, and (4) a precise and robust calibration of projection parameters with group-weighted parameter optimization. Comprehensive experiments conducted on both simulated and real-world datasets demonstrate the robustness, efficiency, and effectiveness of the proposed software.

Benchmarking RNA-Seq Aligners at Base-Level and Junction Base-Level Resolution Using the Arabidopsis thaliana Genome.

The utmost goal of selecting an RNA-Seq alignment software is to perform accurate alignments with a robust algorithm, which is capable of detecting the various intricacies underlying read-mapping procedures and beyond. Most alignment software tools are typically pre-tuned with human or prokaryotic data, and therefore may not be suitable for applications to other organisms, such as plants. The rapidly growing plant RNA-Seq databases call for the assessment of the alignment tools on curated plant data, which will aid the calibration of these tools for applications to plant transcriptomic data. We therefore focused here on benchmarking RNA-Seq read alignment tools, using simulated data derived from the model organism Arabidopsis thaliana. We assessed the performance of five popular RNA-Seq alignment tools that are currently available, based on their usage (citation count). By introducing annotated single nucleotide polymorphisms (SNPs) from The Arabidopsis Information Resource (TAIR), we recorded alignment accuracy at both base-level and junction base-level resolutions for each alignment tool. In addition to assessing the performance of the alignment tools at their default settings, accuracies were also recorded by varying the values of numerous parameters, including the confidence threshold and the level of SNP introduction. The performances of the aligners were found consistent under various testing conditions at the base-level accuracy; however, the junction base-level assessment produced varying results depending upon the applied algorithm. At the read base-level assessment, the overall performance of the aligner STAR was superior to other aligners, with the overall accuracy reaching over 90% under different test conditions. On the other hand, at the junction base-level assessment, SubRead emerged as the most promising aligner, with an overall accuracy over 80% under most test conditions.

Family analysis and literature study of hereditary hypophosphatemic rickets with hypercalciuria

BackgroundHereditary hypophosphatemia rickets with hypercalciuria (HHRH) is a rare autosomal recessive disorder characterised by reduced renal phosphate reabsorption leading to hypophosphataemia, rickets and bone pain. Here, we present a case of HHRH in a Chinese boy.Case presentationWe report a 11-year-old female proband, who was admitted to our hospital with bilateral genuvarum deformity and short stature. Computed Tomography (CT) showed kidney stones, blood tests showed hypophosphatemia, For a clear diagnosis, we employed high-throughput sequencing technology to screen for variants. Our gene sequencing approach encompassed whole exome sequencing, detection of exon and intron junction regions, and examination of a 20 bp region of adjacent introns. Flanking sequences are defined as ±50 bp upstream and downstream of the 5′ and 3′ ends of the coding region.The raw sequence data were compared to the known gene sequence data in publicly available sequence data bases using Burrows-Wheeler Aligner software (BWA, 0.7.12-r1039), and the pathogenic variant sites were annotated using Annovar. Subsequently, the suspected pathogenic variants were classified according to ACMG’s gene variation classification system. Simultaneously, unreported or clinically ambiguous pathogenic variants were predicted and annotated based on population databases. Any suspected pathogenic variants identified through this analysis were then validated using Sanger sequencing technology. At last, the proband and her affected sister carried pathogenic homozygous variant in the geneSLC34A3(exon 13, c.1402C > T; p.R468W). Their parents were both heterozygous carriers of the variant. Genetic testing revealed that the patient has anLRP5(exon 18, c.3917C > T; p.A1306V) variant of Uncertain significance, which is a rare homozygous variant.ConclusionThis case report aims to raise awareness of the presenting characteristics of HHRH. The paper describes a unique case involving variants in both theSLC34A3andLRP5genes, which are inherited in an autosomal recessive manner. This combination of gene variants has not been previously reported in the literature. It is uncertain whether the presence of these two mutated genes in the same individual will result in more severe clinical symptoms. This report shows that an accurate diagnosis is critical, and with early diagnosis and correct treatment, patients will have a better prognosis.

An 800 kyr planktonic δ18O stack for the Western Pacific Warm Pool

Abstract. The Western Pacific Warm Pool (WPWP) exhibits different glacial–interglacial climate variability compared to high latitudes, and its sea surface temperatures are thought to respond primarily to changes in greenhouse forcing. To better characterize the orbital-scale climate response covering the WPWP, we constructed a planktonic δ18O stack (average) of 10 previously published WPWP records of the last 800 kyr, available at https://doi.org/10.5281/zenodo.10211900 (Bowman et al., 2023), using the new Bayesian alignment and stacking software BIGMACS (Lee et al., 2023b). Similarities in stack uncertainty between the WPWP planktonic δ18O stack and benthic δ18O stacks, also constructed using BIGMACS, demonstrate that the software performs similarly well when aligning regional planktonic or benthic δ18O data. A total of 65 radiocarbon dates from the upper portion of five of the WPWP cores suggest that WPWP planktonic δ18O change is nearly synchronous with global benthic δ18O during the last glacial termination. However, the WPWP planktonic δ18O stack exhibits a smaller glacial–interglacial amplitude and less spectral power at all orbital frequencies than benthic δ18O. We assert that the WPWP planktonic δ18O stack provides a useful representation of orbital-scale regional climate response and a valuable regional alignment target, particularly over the 0 to 450 ka portion of the stack.

Statistical framework to determine indel-length distribution.

Insertions and deletions (indels) of short DNA segments, along with substitutions, are the most frequent molecular evolutionary events. Indels were shown to affect numerous macro-evolutionary processes. Because indels may span multiple positions, their impact is a product of both their rate and their length distribution. An accurate inference of indel-length distribution is important for multiple evolutionary and bioinformatics applications, most notably for alignment software. Previous studies counted the number of continuous gap characters in alignments to determine the best-fitting length distribution. However, gap-counting methods are not statistically rigorous, as gap blocks are not synonymous with indels. Furthermore, such methods rely on alignments that regularly contain errors and are biased due to the assumption of alignment methods that indels lengths follow a geometric distribution. We aimed to determine which indel-length distribution best characterizes alignments using statistical rigorous methodologies. To this end, we reduced the alignment bias using a machine-learning algorithm and applied an Approximate Bayesian Computation methodology for model selection. Moreover, we developed a novel method to test if current indel models provide an adequate representation of the evolutionary process. We found that the best-fitting model varies among alignments, with a Zipf length distribution fitting the vast majority of them. The data underlying this article are available in Github, at https://github.com/elyawy/SpartaSim and https://github.com/elyawy/SpartaPipeline.

Potentials of single nucleotide polymorphisms and genetic diversity studies at HSP90AB1 gene in Nigerian White Fulani, Muturu, and N'Dama cattle breeds.

The study was aimed at genetic characterization of Nigerian breeds of Muturu, N'Dama, and White Fulani cattle breeds at heat shock protein 90AB1 locus. Also, the goal of the study was to detect the presence of single nucleotide polymorphisms (SNPs) at HSP90AB1 locus and consequently recommend them as bio-markers for thermo-tolerance potentials in Nigerian cattle breeds when exposed to assaults of thermal conditions/heat shock of tropical environment. Based on the previously published potentials of this candidate gene to lower assaults of thermal conditions/heat shock such as heat stress, the detected SNPs of HSP90AB1 within the population of the Nigerian cattle in this study will be recommended for population-based screening with a view to genetically improving those zebu cattle breeds that are more vulnerable to heat shock and assaults of thermal conditions. Total number of 200 blood samples were randomly collected from White Fulani (84 samples), Muturu (73 samples), and N'Dama (43 samples) breeds of cattle. Out of these, 20 DNA samples were randomly selected from each of the three cattle breeds and were used for DNA extraction and downstream analyses to further confirm findings of previous study, hence the goal of our study. DNA was extracted from the blood samples using the Zymo-bead DNA extraction kit and DNA sequencing of our samples was performed. A total number of 9 SNPs (within exons 5-6 coding regions) and 11 SNPs (within exons 12-13 coding regions) were detected at HSP90AB1 locus using the codon code aligner software. ARLEQUIN 2.0001 software was used to estimate the basic population genetic statistics while the DnaSP version 5.10.01 was used to estimate the genetic diversity indices. This study detected new SNPs (polymorphic sites) at HSP90AB1 locus within the DNAs of Nigerian White Fulani (WF), Muturu (MU), and N'Dama (ND) breeds of cattle. Within exons 5-6 coding regions, the N'Dama (ND) cattle breed had the highest for number of SNPs (5) and genetic diversity indices while White Fulani (WF) and Muturu (MU) had the least (2) number of SNPs each. Within exons 12-13 coding regions, WF had the highest numbers of SNPs (7) and genetic diversity indices while MU had the least number of SNPs (1) and genetic diversity indices. Some of the detected SNPs at HSP90AB1 locus were shared among the three breeds, suggesting that these three Nigerian cattle breeds showed shared ancestral alleles and lineage. Our study further revealed that HSP90AB1 is highly polymorphic/variable and diverse among the three Nigerian cattle breeds examined. Based on the previously documented thermo-tolerance potentials of members of HSP90 sub-family including the findings of our study, we hypothesize therefore that the presence of SNPs of HSP90AB1 within the DNAs of these three breeds of Nigerian cattle (WF, ND, and MU) may confer them thermo-tolerance potentials for thermal assault conditions and heat shock of the tropics at HSP90AB1 locus. Therefore, the detected SNPs can be recommended as bio-markers to improve the thermo-tolerance potentials of Nigerian breeds of zebu cattle raised under the challenges of heat shock for better adaptation and survival.

Genetic analysis of isolated methylmalonic acidemia in Henan, China: c.1663G>A variant of MMUT prevalent in the Henan population

BackgroundMethylmalonic acidemia (MMA) is the most common organic acidemia in China, and isolated MMA accounts for approximately 30 % of all types of MMA. Common variants of the MMUT gene vary greatly around the world. The present study aims to determine the high-frequency and novel genetic variants of the MMUT gene in the Henan population of China and evaluate the prognosis of patients carrying the c.1663G>A (p.Ala555Thr) variant. MethodsWe performed next-generation sequencing for 41 patients with isolated MMA screened by tandem mass spectrometry (MS/MS) and analysed the genetic results. We also evaluated the prognosis of patients with the c.1663G>A variant. We used Jalview software for multispecies sequence alignment and Missense3D and DynaMut to predict the protein function of the detected novel variants. ResultsA total of 43 variants from 41 patients with isolated MMA were detected, of which c.1663G>A (14.63 %), c.729_730insTT (10.98 %), and c.1106G>A (8.53 %) are high-frequency variants of the MMUT gene in the Henan population. The patients carrying the c.1663G>A variant tended to be responsive to vitamin B12, have a low mortality rate. We also identified 5 novel variants (c.479C>T, c.811G>C, c.965T>A, c.1142G>A and c.1667C>T). ConclusionThe rare variant c.1663G>A is prevalent in the Henan population, and infants with this variant tend to have good prognosis. Our findings, especially novel variants, will help broaden the spectrum of genetic variants and facilitate clinical diagnosis and genetic counselling for affected families.

Influence of scanbody design and intraoral scanner on the trueness of complete arch implant digital impressions: An in vitro study.

This study aimed to compare the accuracy of full-arch digital implant impressions using seven different scanbodies and four intraoral scanners. A 3D-printed maxillary model with six implants and their respective multi-unit abutments was used for this study. Seven scanbodies (SB1, SB2, SB3, SB4, SB5, SB6, and SB7) and four intraoral scanners (Primescan®, Omnican®, Trios 3®, and Trios 4®) were assessed. Each combination group was scanned ten times and a dental lab scanner (D2000, 3Shape) was used as a reference. All scans were exported as STL files, imported into Convince software (3Shape) for alignment, and later into Blender software, where their 3D positions were analyzed using a Python script. The 3D deviation, angular deviation, and linear distance between implants #3 and #14 were also measured. Accuracy was measured in terms of "trueness" (scanbody 3D deviation between intraoral scan and desktop scan). Kruskal-Wallis followed by the Bonferroni correction was used to analyze the data (⍺ = .05). The study found statistically significant differences in digital impression accuracy among the scanners and scanbodies (p<0.001). When comparing different intraoral scanners, the Primescan system showed the smallest 3D deviation (median 110.59 μm) and differed statistically from the others, while Trios 4 (median 122.35 μm) and Trios 3 (median 130.62 μm) did not differ from each other (p = .284). No differences were found in the linear distance between implants #3 and #14 between Trios 4, Primescan, and Trios 3 systems. When comparing different scanbodies, the lowest median values for 3D deviation were obtained by SB2 (72.27μm) and SB7 (93.31μm), and they did not differ from each other (p = .116). The implant scanbody and intraoral scanner influenced the accuracy of digital impressions on completely edentulous arches.

A Comparative Study of Antibacterial Activity of Leaf and Root Extracts of Sida acuta Burm. F. Against Staphylococcus sciuri Isolated From Acne Using Computer-Aided Technique

This study investigated the significant anti-bacteriological efficacy between leaf and root of Sida acuta Burm. F. extracts against acne inducing bacteria. Twelve samples were collected from twelve persons with facial acne. Nutrient agar was used for the isolation of the bacteria and 16S rRNA gene sequencing technique was used for molecular identification. Bioinformatics analysis was carried out using Basic Local Alignment Search Tools (BLAST) for similarity, Cluster W software for multiple sequence alignment and MEGA 7 software for the phylogenetic analysis. Antibacterial susceptibility test of the bacterial isolates was carried out using the agar well diffusion method. A total number of six bacterial species were identified as Staphylococcus sciuri. The study revealed that control antibiotic- Ciprofloxacin (CFX) inhibited the growth of all the bacterial isolates. Staphylococcus sciuri was susceptible to leaf ethanol extract of Sida acuta at 75 μg/ml and 100 μg/ml and was susceptible to the aqueous root extract at 25 μg/ml and 100 μg/ml while it was susceptible to the ethanol root extract at 2.5 μg/ml. From this study, it was shown that the aqueous root extracts had more zones of inhibition with the maximum inhibition of 45mm at 100 μg/ml. Hence, Sida acuta Burm. F. is a powerful antimicrobial agent.

Efficient end-to-end long-read sequence mapping using minimap2-fpga integrated with hardware accelerated chaining

minimap2 is the gold-standard software for reference-based sequence mapping in third-generation long-read sequencing. While minimap2 is relatively fast, further speedup is desirable, especially when processing a multitude of large datasets. In this work, we present minimap2-fpga, a hardware-accelerated version of minimap2 that speeds up the mapping process by integrating an FPGA kernel optimised for chaining. Integrating the FPGA kernel into minimap2 posed significant challenges that we solved by accurately predicting the processing time on hardware while considering data transfer overheads, mitigating hardware scheduling overheads in a multi-threaded environment, and optimizing memory management for processing large realistic datasets. We demonstrate speed-ups in end-to-end run-time for data from both Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio). minimap2-fpga is up to 79% and 53% faster than minimap2 for sim 30times ONT and sim 50times PacBio datasets respectively, when mapping without base-level alignment. When mapping with base-level alignment, minimap2-fpga is up to 62% and 10% faster than minimap2 for sim 30times ONT and sim 50times PacBio datasets respectively. The accuracy is near-identical to that of original minimap2 for both ONT and PacBio data, when mapping both with and without base-level alignment. minimap2-fpga is supported on Intel FPGA-based systems (evaluations performed on an on-premise system) and Xilinx FPGA-based systems (evaluations performed on a cloud system). We also provide a well-documented library for the FPGA-accelerated chaining kernel to be used by future researchers developing sequence alignment software with limited hardware background.

Performance and Quality Comparison of Movie Alignment Software for Cryogenic Electron Microscopy.

Cryogenic electron microscopy (Cryo-EM) has been established as one of the key players in structural biology. It can reconstruct a 3D model of a sample at a near-atomic resolution. With the increasing number of facilities, faster microscopes, and new imaging techniques, there is a growing demand for algorithms and programs able to process the so-called movie data produced by the microscopes in real time while preserving a high resolution and maximal information. In this article, we conduct a comparative analysis of the quality and performance of the most commonly used software for movie alignment. More precisely, we compare the most recent versions of FlexAlign (Xmipp v3.23.03), MotionCor2 (v1.6.4), Relion MotionCor (v4.0-beta), Warp (v1.0.9), and CryoSPARC (v4.0.3). We tested the quality of the alignment using generated phantom data, as well as real datasets, comparing the alignment precision, power spectra density, and performance scaling of each program.

BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data

BackgroundBisulfite sequencing is a powerful tool for profiling genomic methylation, an epigenetic modification critical in the understanding of cancer, psychiatric disorders, and many other conditions. Raw data generated by whole genome bisulfite sequencing (WGBS) requires several computational steps before it is ready for statistical analysis, and particular care is required to process data in a timely and memory-efficient manner. Alignment to a reference genome is one of the most computationally demanding steps in a WGBS workflow, taking several hours or even days with commonly used WGBS-specific alignment software. This naturally motivates the creation of computational workflows that can utilize GPU-based alignment software to greatly speed up the bottleneck step. In addition, WGBS produces raw data that is large and often unwieldy; a lack of memory-efficient representation of data by existing pipelines renders WGBS impractical or impossible to many researchers.ResultsWe present BiocMAP, a Bioconductor-friendly methylation analysis pipeline consisting of two modules, to address the above concerns. The first module performs computationally-intensive read alignment using Arioc, a GPU-accelerated short-read aligner. Since GPUs are not always available on the same computing environments where traditional CPU-based analyses are convenient, the second module may be run in a GPU-free environment. This module extracts and merges DNA methylation proportions—the fractions of methylated cytosines across all cells in a sample at a given genomic site. Bioconductor-based output objects in R utilize an on-disk data representation to drastically reduce required main memory and make WGBS projects computationally feasible to more researchers.ConclusionsBiocMAP is implemented using Nextflow and available at http://research.libd.org/BiocMAP/. To enable reproducible analysis across a variety of typical computing environments, BiocMAP can be containerized with Docker or Singularity, and executed locally or with the SLURM or SGE scheduling engines. By providing Bioconductor objects, BiocMAP’s output can be integrated with powerful analytical open source software for analyzing methylation data.

Short-read aligner performance in germline variant identification.

Read alignment is an essential first step in the characterization of DNA sequence variation. The accuracy of variant calling results depends not only on the quality of read alignment and variant calling software but also on the interaction between these complex software tools. In this review, we evaluate short-read aligner performance with the goal of optimizing germline variant calling accuracy. We examine the performance of three general-purpose short-read aligners - BWA-MEM, Bowtie 2, and Arioc - in conjunction with three germline variant callers: DeepVariant, FreeBayes, and GATK HaplotypeCaller. We discuss the behavior of the read aligners with regard to the data elements on which the variant callers rely, and illustrate how the runtime configurations of these software tools combine to affect variant calling performance. The quick brown fox jumps over the lazy dog. Supplementary information is available at Bioinformatics online.

A comparison of hydrophilic interaction liquid chromatography and capillary electrophoresis for the metabolomics analysis of human serum

Cationic, anionic, zwitterionic and, partially polar metabolites are very important constituents of blood serum. Several of these metabolites underpin the core metabolism of cells (e.g., Krebs cycle, urea cycle, proteins synthesis, etc.), while others might be considered ancillary but still important to grasp the status of any organism through blood serum analysis. Due to its wide chemical diversity, modern metabolomics analysis of serum is still struggling to provide a complete and comprehensive picture of the polar metabolome, due to the limitations of each specific analytical method. In this study, two metabolomics-based analytical methods using the most successful techniques for polar compounds separation in human serum samples, namely hydrophilic interaction liquid chromatography (HILIC) and capillary electrophoresis (CE), are evaluated, both coupled to a high-resolution time-of-flight mass spectrometer via electrospray ionization (ESI-Q-TOF-MS). The performance of the two methods have been compared using five terms of comparison, three of which are specific to metabolomics, such as (1) compounds’ detectability (2) Pezzatti score (Pezzatti et al. 2018), (3) intra-day precision (repeatability), (4) ease of automatic analysis of the data (through a common deconvolution alignment and extrapolation software, MS-DIAL, and (5) time & cost analysis. From this study, HILIC-MS proved to be a better tool for polar metabolome analysis, while CE-MS helped identify some interesting variables that gave it interest in completing metabolome coverage in metabolomics studies. Finally, in this framework, MS-DIAL demonstrates for the first time its ability to process CE data for metabolomics, although it is not designed for it.

In silico analysis of potential loci for the identification of Vanda spp. in the Philippines

Difficulties in identifying Vanda species are still encountered, and the ambiguity in its taxonomy is still unresolved. To date, the advancement in molecular genetics technology has given rise to the molecular method for plant identification and elucidation. One hundred twenty-five (125) gene sequences of Vanda species from the Philippines were obtained from the NCBI GenBank. Four of the 25 loci were further examined using MEGA 11 software for multiple sequence alignment, sequence analysis, and phylogenetic reconstruction. The indel-based and tree-based methods were combined to compute the species resolution. The result showed that ITS from the nuclear region obtained the highest species resolution with 66.67%. It was then followed by psbA-trnH, matK, and trnL-trnF from the chloroplast genome with a species resolution of 60%, 40%, and 30.77%, respectively. ITS and psbA-trnH satisfied the ideal length for DNA barcoding as they have 655 bp and 701 bp, respectively. The locus psbA-trnH was also considered to have a higher potential to discriminate Vanda species since only a few sequences were tested for ITS. Furthermore, ITS and trnL-trnF have the highest variable rate, which is 2.9%, while matK and psbA-trnH have 2% and 1.3%, respectively. This showed the nature of the unique sequences of various species. In this study, the indel-based method provided better results than the tree-based method. It will help support further DNA barcoding studies and strengthen the conservation and protection of Vanda spp. in the Philippines.

Novel variants in the PAX6 gene related to isolated aniridia.

Aniridia, which is a rare congenital defect of the eye, consists of iris hypoplasia or aplasia, and additional ocular abnormalities. It is most commonly caused by autosomal dominant PAX6 gene mutations. However, in about 30% of cases, it is associated with chromosomal rearrangements in the 11p13 region. The aim of this study was to identify the potential PAX6 gene variants, which could cause the isolated aniridia. Eight patients with isolated aniridia were included in this study. MLPA analysis allowed in the past to exclude large structural rearrangements of the PAX6 and adjacent genes like WT1. Blood samples were collected from the patients (and their families in familial cases) and genomic DNA was extracted from peripheral blood leukocytes and buccal cells. The amplification of the 11 exons of the PAX6 gene was performed. Bidirectional Sanger Sequencing was conducted for the identification of the potentially pathogenic variants, and for the segregation analysis of the identified variant in the family. The results were analyzed with the use of CodonCode Aligner software. In three patients, aniridia was sporadic, whereas in another five cases, the eye defect was familial. The potentially pathogenic variants in the PAX6 gene were found in 6 out of 8 patients with aniridia. We identified four known (c.781C > T, c.607C > T, and c.949C > T twice), and two novel variants (c.258_265del and c.495_496insG). Point mutations in the PAX6 gene are the most frequent cause of aniridia. The investigation of the genetic background of the disease is essential for patients to evaluate recurrence risk in the offspring.

Comparison of some Alignment Software in the Analysis of Dairy Cows RNA-Seq Data

Comparison of some Alignment Software in the Analysis of Dairy Cows RNA-Seq Data

Evaluation of Different SNP Analysis Software and Optimal Mining Process in Tree Species.

Single nucleotide polymorphism (SNP) is one of the most widely used molecular markers to help researchers understand the relationship between phenotypes and genotypes. SNP calling mainly consists of two steps, including read alignment and locus identification based on statistical models, and various software have been developed and applied in this issue. Meanwhile, in our study, very low agreement (<25%) was found among the prediction results generated by different software, which was much less consistent than expected. In order to obtain the optimal protocol of SNP mining in tree species, the algorithm principles of different alignment and SNP mining software were discussed in detail. And the prediction results were further validated based on in silico and experimental methods. In addition, hundreds of validated SNPs were provided along with some practical suggestions on program selection and accuracy improvement were provided, and we wish that these results could lay the foundation for the subsequent analysis of SNP mining.

Ubiquitous conservative interaction patterns between post-spliced introns and their mRNAs revealed by genome-wide interspecies comparison.

Introns, as important vectors of biological functions, can influence many stages of mRNA metabolism. However, in recent research, post-spliced introns are rarely considered. In this study, the optimal matched regions between introns and their mRNAs in nine model organism genomes were investigated with improved Smith-Waterman local alignment software. Our results showed that the distributions of mRNA optimal matched frequencies were highly consistent or universal. There are optimal matched frequency peaks in the UTR regions, which are obvious, especially in the 3'-UTR. The matched frequencies are relatively low in the CDS regions of the mRNA. The distributions of the optimal matched frequencies around the functional sites are also remarkably changed. The centers of the GC content distributions for different sequences are different. The matched rate distributions are highly consistent and are located mainly between 60% and 80%. The most probable value of the optimal matched segments is about 20bp for lower eukaryotes and 30bp for higher eukaryotes. These results show that there are abundant functional units in the introns, and these functional units are correlated structurally with all kinds of sequences of mRNA. The interaction between the post-spliced introns and their corresponding mRNAs may play a key role in gene expression.