Identification of Non-Coding RNAs Based on Alignment-Free Features in Crassostrea gigas(Pacific Oyster)Transcriptome

Non-coding RNAs(ncRNAs)play important roles in the regulation of many biological processes,such as transcription initiation and epigenetic modifications that occur after transcription and development.Several novel transcripts have been identified via high-throughput sequencing.However,identifying ncRNAs among the transcripts of novel species using alignment-based features is difficult.Thus,developing a fast and accurate method based on alignment-free features to identify ncRNAs among novel transcripts is necessary.In this study,we proposed a new approach,namely,coding potential prediction based on alignment-free features(CPAF),to identify ncRNAs among a large number of candidates.CPAF used four types of features:Fickett score;Hexamer score;composition,transition,and distribution features;and modified k-mer.From the results,CPAF performed better than previous state-of-the-art methods in predicting ncRNA transcripts,with particular reference to small ncRNAs.Finally,we applied CPAF to identify ncRNAs in Pacific oyster transcripts.Our approach identified more ncRNAs than other previously used methods.

CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy

A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http：//tlife.fudan.edu.cn/cvtree3/without login requirements.

Large-range alignment-free distributed-cavity laser based on an improved multi-lens retrorefleetor

A multi-lens retroreflector with field curvature compensation was designed and used in an alignment-free distributed-cavity laser with a long working distance for resonant beam charging applications.The multi-lens design,which makes use of off-the-shelf components,also allows a large field of view[FoV]without requirement of large element aperture.By implementing this design,an end-pumped 1063 nm Nd:GdVO4 laser could deliver over 5 W continuous-wave output power over a large range of working distances(1-5 m)and with ±30°receiver FoV under an incident diode pump power of 16.6 W.The output power fluctuation was less than 10%when moving and tilting the receiver over such a large range,without requiring any realignment of the cavity.

CVTree: A Parallel Alignment-free Phylogeny and Taxonomy Tool Based on Composition Vectors of Genomes

Composition Vector Tree(CVTree) is an alignment-free algorithm to infer phylogenetic relationships from genome sequences. It has been successfully applied to study phylogeny and taxonomy of viruses, prokaryotes, and fungi based on the whole genomes, as well as chloroplast genomes, mitochondrial genomes, and metagenomes. Here we presented the standalone software for the CVTree algorithm. In the software, an extensible parallel workflow for the CVTree algorithm was designed. Based on the workflow, new alignment-free methods were also implemented. And by examining the phylogeny and taxonomy of 13,903 prokaryotes based on 16 S r RNA sequences, we showed that CVTree software is an efficient and effective tool for studying phylogeny and taxonomy based on genome sequences. The code of CVTree software can be available at https://github.com/ghzuo/cvtree.

The statistical power of k-mer based aggregative statistics for alignment-free detection of horizontal gene transfer

Alignment-based database search and sequence comparison are commonly used to detect horizontal gene transfer(HGT).However,with the rapid increase of sequencing depth,hundreds of thousands of contigs are routinely assembled from metagenomics studies,which challenges alignment-based HGT analysis by overwhelming the known reference sequences.Detecting HGT by k-mer statistics thus becomes an attractive alternative.These alignment-free statistics have been demonstrated in high performance and efficiency in wholegenome and transcriptome comparisons.To adapt k-mer statistics for HGT detection,we developed two aggregative statistics T^(S)_(sum ) and T^(*)_(sum),which subsample metagenome contigs by their representative regions,and summarize the regional D^(S) _(2) and D^(*)_(2)metrics by their upper bounds.We systematically studied the aggregative statistics’power at different k-mer size using simulations.Our analysis showed that,in general,the power of T^(S)_(sum) and T^(*)_(sum) increases with sequencing coverage,and reaches a maximum power>80%at k=6,with 5%Type-I error and the coverage ratio>0.2x.The statistical power ofT^(S)_(sum) and T^(*)_(sum) was evaluated with realistic simulations of HGT mechanism,sequencing depth,read length,and base error.We expect these statistics to be useful distance metrics for identifying HGT in metagenomic studies.

Wearable Alignment‑Free Microfber‑Based Sensor Chip for Precise Vital Signs Monitoring and Cardiovascular Assessment

Continuous pulse wave signals monitoring is the essential basis for clinical cardiovascular diagnosis and treatment.Recent researches show the majority of current electronic pulse sensors usually face challenges in electrical safety concern,poor durability and demanding precision in position alignment.Thus,a highly sensitive,inherently electrical safe,robust and alignment-free device is highly desired.Here,we present a wearable alignment-free microfber-based sensor chip(AFMSC)for precise vital signs monitoring and cardiovascular health assessment.The AFMSC comprises an optical micro/nano fber sensor(MNF)and a fexible soft liquid sac while the MNF sensor is used to perceive the physiological signals and the liquid sac is used to eliminate the misalignment.The real-time and accurate monitoring of the pulse signals was realized by tracking the optical power variation of transmitted light from MNF.Then,the cardiovascular vital signs extracted from radial artery pulse signals were used to evaluate cardiovascular health condition and the results were in accordance with human physiological characteristics.Moreover,the pulse signals from diferent arterial area,the respiration signals from chest and the radial pulse signals before and after exercise were detected and analyzed.The non-invasive,continuous and accurate monitoring of cardiovascular health based on the reported wearable and alignment-free device is promising in both ftness monitoring and medical diagnostics for cardiovascular disease prevention and diagnosis.