大孢虫花菌丝体多糖提取工艺优化及其测定方法优选

通过采用3,5-二硝基水杨酸法、蒽酮-硫酸法和苯酚-硫酸法测定大孢虫花PaecilomycestenuipesPeck菌丝体多糖含量,比较精密度、样品回收率、稳定性三个指标,得出最佳测定方法为蒽酮-硫酸法。根据一次一因素实验和Box-Behnken中心组合实验,应用SAS软件分析得出大孢虫花菌丝体多糖提取的最佳条件为:100℃沸水浴,提取2h,重复4次,料液比(菌丝体质量:蒸馏水体积)为1︰20,此条件下大孢虫花菌丝体多糖为4.12g/100g。     

Vector NTI, a balanced all-in-one sequence analysis suite

Vector NTI is a well-balanced desktop application integrated for molecular sequence analysis and biological data management. It has a centralised database and five application modules: Vector NTI, AlignX, BioAnnotator, ContigExpress and GenomBench. In this review, the features and functions available in this software are examined. These include database management, primer design, virtual cloning, alignments, sequence assembly, 3D molecular viewer and internet tools. Some problems encountered when using this software are also discussed. It is hoped that this review will introduce this software to more molecular biologists so they can make better-informed decisions when choosing computational tools to facilitate their everyday laboratory work. This tool can save time and enhance analysis but it requires some learning on the user's part and there are some issues that need to be addressed by the developer.     

Comparative evaluation of microarray analysis software

A wide variety of software tools are available to analyze microarray data. To identify the optimum software for any project, it is essential to define specific and essential criteria on which to evaluate the advantages of the key features. In this review we describe the results of our comparison of several software tools. We then conclude with a discussion of the subset of tools that are most commonly used and describe the features that would constitute the “ideal microarray analysis software suite.”     

On the parallelisation of bioinformatics applications

This paper surveys the computational strategies followed to parallelise the most used software in the bioinformatics arena. The studied algorithms are computationally expensive and their computational patterns range from regular, such as database-searching applications, to very irregularly structured patterns (phylogenetic trees). Fine- and coarse-grained parallel strategies are discussed for these very diverse sets of applications. This overview outlines computational issues related to parallelism, physical machine models, parallel programming approaches and scheduling strategies for a broad range of computer architectures. In particular, it deals with shared, distributed and shared/distributed memory architectures.     

Program MULDER -- a tool for extracting torsion angles from NMR data

MULDER (Mostly UniversaL Dihedral angle ExtractoR) is a program for extraction of torsion angle information from NMR data. Currently, it can analyze two types of input data: The torsion angle data, where several ³J-coupling constants and/or interatomic distances are combined in order to reduce the torsion angle ambiguity arising from solving the isolated Karplus (or distance) equation, and the sugar pucker data, where the dynamics of five-membered sugar rings is evaluated by postprocessing the results calculated from ³J_(HH) coupling constants by program PSEUROT. Program MULDER can be used either as an alternative to r-MD programs in situations where only specific structural features are studied, or as a preparatory tool in connection with full r-MD structure calculation for extraction of unambiguous torsion angle restraints.     

Protein family alignment annotation

For bioscientists studying protein structure and function, the Protein Family Alignment Annotation Tool (Pfaat) is a useful and simple program for annotating collections of proteins. This open-source software includes methods for viewing and aligning protein families, and for annotating sequence structure and residues with known functions. It offers new options to aid the study of proteins, and an extensible annotation tool for bioinformatics developers.     

Viewing and annotating sequence data with Artemis

Artemis is a widely used software tool for annotating and viewing sequence data. No database is required to use Artemis. Instead, individual sequence data files can be analysed with little or no formatting, making it particularly suited to the study of small genomes and chromosomes, and straightforward for a novice user to get started. Since its release in 1999, Artemis has been used to annotate a diverse collection of prokaryotic and eukaryotic genomes, ranging from Streptomyces coelicolor to, more recently, a large proportion of the Plasmodium falciparum genome. Artemis allows annotated genomes to be easily browsed and makes it simple to add useful biological information to raw sequence data. This paper gives an overview of some of the features of Artemis and includes how it facilitates manual gene prediction and can provide an overview of entire chromosomes or small compact genomes--useful for uncovering unusual features such as pathogenicity islands.     

ITMSQ: A software tool for N‐ and C‐terminal fragment ion pairs based isobaric tandem mass spectrometry quantification

Tandem MS (MS2) quantification using the series of N‐ and C‐terminal fragment ion pairs generated from isobaric‐labelled peptides was recently considered an accurate strategy in quantitative proteomics. However, the presence of multiplexed terminal fragment ion in MS2 spectra may reduce the efficiency of peptide identification, resulting in lower identification scores or even incorrect assignments. To address this issue, we developed a quantitative software tool, denoted isobaric tandem MS quantification (ITMSQ), to improve N‐ and C‐terminal fragment ion pairs based isobaric MS2 quantification. A spectrum splitting module was designed to separate the MS2 spectra from different samples, increasing the accuracy of both identification and quantification. ITMSQ offers a convenient interface through which parameters can be changed along with the labelling method, and the result files and all of the intermediate files can be exported. We performed an analysis of in vivo terminal amino acid labelling labelled HeLa samples and found that the numbers of quantified proteins and peptides increased by 13.64 and 27.52% after spectrum splitting, respectively. In conclusion, ITMSQ provides an accurate and reliable quantitative solutionfor N‐ and C‐terminal fragment ion pairs based isobaric MS2 quantitative methods.     

DomeTree: a canonical toolkit for mitochondrial DNA analyses in domesticated animals

Mitochondrial DNA (mtDNA) is widely used in various genetic studies of domesticated animals. Many applications require comprehensive knowledge about the phylogeny of mtDNA variants. Herein, we provide the most up‐to‐date mtDNA phylogeny (i.e. haplogroup tree or matrilineal genealogy) and a standardized hierarchical haplogroup nomenclature system for domesticated cattle, dogs, goats, horses, pigs, sheep, yaks and chickens. These high‐resolution mtDNA haplogroup trees based on 1240 complete or near‐complete mtDNA genome sequences are available in open resource DomeTree ( http://www.dometree.org ). In addition, we offer the software MitoToolPy ( http://www.mitotool.org/mp.html ) to facilitate the mtDNA data analyses. We will continuously and regularly update DomeTree and MitoToolPy.