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Method for Assessing the Statistical Significance of Mass Spectral Similarities Using basic local alignment search tool Statistics

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ANALYTICAL CHEMISTRY 2013年第17期85卷 8291-8297页

作者： Matsuda, Fumio Tsugawa, Hiroshi Fukusaki, Eiichiro Osaka Univ Grad Sch Informat Sci & Technol Dept Bioinformat Engn Suita Osaka 5650871 Japan Osaka Univ Grad Sch Engn Dept Biotechnol Suita Osaka 5650871 Japan RIKEN Ctr Sustainable Resource Sci Turumi Ku Yokohama Kanagawa 2300045 Japan

A novel method for assessing the statistical significance of mass spectral similarities was developed using modified basic local alignment search tool (BLAST;Karlin- Altschul) statistics. In gas chromatography/mass spectrometry-based metabolomics, many signals in raw metabolome data are identified on the basis of unexpected similarities among mass spectra and the spectra of standards. Since there is inevitably noise in the observed spectra, a list of identified metabolites includes some false positives. In the developed method, electron ionization (El) mass spectrometry-BLAST, a similarity score of two mass spectra is calculated using a general scoring scheme, from which the probability of obtaining the score by chance (P value) is calculated. For this purpose, a simple rule for converting a unit El mass spectrum to a mass spectral sequence as well as a score matrix for aligned mass spectral sequences was developed. A Monte Carlo simulation using randomly generated mass spectral sequences demonstrated that the null distribution or the expected number of hits (E value) follows modified Karlin-Altschul statistics. A metabolite data set obtained from green tea extract was analyzed using the developed method. Among 171 metabolite signals in the metabolome data, 93 signals were identified on the basis of significant similarities (P < 0.015) with reference data. Since the expected number of false positives is 2.6, the false discovery rate was estimated to be 2.8%, indicating that the search threshold (P < 0.015) is reasonable for metabolite identification.

关键词： mass basic local alignment search tool mass spectra Metabolome Analogy False-positives Monte Carlo technique Green Tea Extract Statistical Significance metabolites

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*** network distributed basic local alignment search toolkit (***-BLAST)

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BMC BIOINFORMATICS 2005年第1期6卷 93-93页

作者： Dowd, SE Zaragoza, J Rodriguez, JR Oliver, MJ Payton, PR ARS Livestock Issues Res Unit USDA Lubbock TX USA ARS Plant Stress & Germplasm Dev Res Unit USDA Lubbock TX USA

Background: BLAST is one of the most common and useful tools for Genetic Research. This paper describes a software application we have termed Windows. NET Distributed basic local alignment search toolkit ( W. ND-BLAST), which enhances the BLAST utility by improving usability, fault recovery, and scalability in a Windows desktop environment. Our goal was to develop an easy to use, fault tolerant, high-throughput BLAST solution that incorporates a comprehensive BLAST result viewer with curation and annotation functionality. Results: ***-BLAST is a comprehensive Windows-based software toolkit that targets researchers, including those with minimal computer skills, and provides the ability increase the performance of BLAST by distributing BLAST queries to any number of Windows based machines across local area networks (LAN). ***-BLAST provides intuitive Graphic User Interfaces (GUI) for BLAST database creation, BLAST execution, BLAST output evaluation and BLAST result exportation. This software also provides several layers of fault tolerance and fault recovery to prevent loss of data if nodes or master machines fail. This paper lays out the functionality of ***-BLAST. ***-BLAST displays close to 100% performance efficiency when distributing tasks to 12 remote computers of the same performance class. A high throughput BLAST job which took 662.68 minutes ( 11 hours) on one average machine was completed in 44.97 minutes when distributed to 17 nodes, which included lower performance class machines. Finally, there is a comprehensive high-throughput BLAST Output Viewer (BOV) and Annotation Engine components, which provides comprehensive exportation of BLAST hits to text files, annotated fasta files, tables, or association files. Conclusion: ***-BLAST provides an interactive tool that allows scientists to easily utilizing their available computing resources for high throughput and comprehensive sequence analyses. The install package for ***-BLAST is freely downloadable fr

关键词： Fault Tolerance Child Node basic local alignment search tool Master Node Fasta File

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Using genomic resources to guide research directions. The arabinogalactan protein gene family as a test case

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PLANT PHYSIOLOGY 2002年第4期129卷 1448-1463页

作者： Schultz, CJ Rumsewicz, MP Johnson, KL Jones, BJ Gaspar, YM Bacic, A Univ Adelaide Waite Agr Res Inst Dept Plant Sci Glen Osmond SA 5064 Australia Univ Melbourne Sch Bot Plant Cell Biol Res Ctr Melbourne Vic 3010 Australia

Arabinogalactan proteins (AGPs) are extracellular hydroxyproline-rich proteoglycans implicated in plant growth and development. The protein backbones of AGPs are rich in proline/hydroxyproline, serine, alanine, and threonine. Most family members have less than 40% similarity;therefore, finding family members using basic local alignment search tool searches is difficult. As part of our systematic analysis of AGP function in Arabidopsis, we wanted to make sure that we had identified most of the members of the gene family. We used the biased amino acid composition of AGPs to identify AGPs and arabinogalactan (AG) peptides in the Arabidopsis genome. Different criteria were used to identify the fasciclin-like AGPs. In total, we have identified 13 classical AGPs, 10 AG-peptides, three basic AGPs that include a short lysine-rich region, and 21 fasciclin-like AGPs. To streamline the analysis of genomic resources to assist in the planning of targeted experimental approaches, we have adopted a flow chart to maximize the information that can be obtained about each gene. One of the key steps is the reformatting of the Arabidopsis Functional Genomics Consortium microarray data. This customized software program makes it possible to view the ratio data for all Arabidopsis Functional Genomics Consortium experiments and as many genes as desired in a single spreadsheet. The results for reciprocal experiments are grouped to simplify analysis and candidate AGPs involved in development or biotic and abiotic stress responses are readily identified. The microarray data support the suggestion that different AGPs have different functions.

关键词： Hydroxyproline-rich glycoproteins Expressed sequence tags Gum-arabic glycoprotein T-dna Nicotiana-alata Arabidopsis-thaliana Reverse genetics Pyrus-communis Extracellular-matrix Functional genomics basic local alignment search tool CASING INSPECTION Nicotiana alata Gene families Expressed Sequence Tags Glycoproteins Reformatting Genetics Arabidopsis Amino acid composition functional/structural genomics arabinogalactan T-DNA Family Members

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Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis

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BMC BIOINFORMATICS 2007年第1期8卷 1-14页

作者： Liu, Chun-Chi Lin, Chin-Chung Li, Ker-Chau Chen, Wen-Shyen E. Chen, Jiun-Ching Yang, Ming-Te Yang, Pan-Chyr Chang, Pei-Chun Chen, Jeremy J. W. Natl Chung Hsing Univ Dept Comp Sci Taichung Taiwan Natl Chung Hsing Univ Inst Biomed Sci Taichung Taiwan Acad Sinica Inst Stat Sci Taipei Taiwan Natl Chung Hsing Univ Inst Mol Biol Taichung Taiwan Natl Taiwan Univ Coll Med NTU Ctr Genom Med Taipei 10764 Taiwan Asia Univ Dept Biotechnol & Bioinformat Taichung Taiwan

Background: Genome-wide identification of specific oligonucleotides (oligos) is a computationally-intensive task and is a requirement for designing microarray probes, primers, and siRNAs. An artificial neural network ( ANN) is a machine learning technique that can effectively process complex and high noise data. Here, ANNs are applied to process the unique subsequence distribution for prediction of specific oligos. Results: We present a novel and efficient algorithm, named the integration of ANN and BLAST (IAB) algorithm, to identify specific oligos. We establish the unique marker database for human and rat gene index databases using the hash table algorithm. We then create the input vectors, via the unique marker database, to train and test the ANN. The trained ANN predicted the specific oligos with high efficiency, and these oligos were subsequently verified by BLAST. To improve the prediction performance, the ANN over-fitting issue was avoided by early stopping with the best observed error and a k-fold validation was also applied. The performance of the IAB algorithm was about 5.2, 7.1, and 6.7 times faster than the BLAST search without ANN for experimental results of 70-mer, 50-mer, and 25-mer specific oligos, respectively. In addition, the results of polymerase chain reactions showed that the primers predicted by the IAB algorithm could specifically amplify the corresponding genes. The IAB algorithm has been integrated into a previously published comprehensive web server to support microarray analysis and genome-wide iterative enrichment analysis, through which users can identify a group of desired genes and then discover the specific oligos of these genes. Conclusion: The IAB algorithm has been developed to construct SpecificDB, a web server that provides a specific and valid oligo database of the probe, siRNA, and primer design for the human genome. We also demonstrate the ability of the IAB algorithm to predict specific oligos through polymerase chain reacti

关键词： Root Mean Square Error Artificial Neural Network basic local alignment search tool Specific Oligos Hide Layer Node

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Identification of taxol biosynthesis stage-enriched transcripts in Nodulisporium sylviforme, using suppression subtractive hybridization

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WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY 2008年第11期24卷 2601-2605页

作者： Chi, Yan Zhao, Dong-Li Zhou, Dong-Po Heilongjiang Univ Key Lab Microbe Harbin Peoples R China Dalian Univ Coll Biol Engn Key Lab Bioorgan Chem Dalian Peoples R China Dalian Univ Coll Med Dalian Peoples R China

The endophytic fungus Nodulisporium sylviforme produces taxol, a diterpene alkaloid compound that has unique anti-neoplastic activity. In this study, suppression subtractive hybridization was performed to identify genes in N. sylviforme that were involved in the up-regulation of taxol production. A total of 91 clones represented the differentially expressed genes were selected based on reverse blotting results. These clones were then sequenced and analyzed using BLAST-X comparisons that revealed that about 37.8% of the ESTs were homologous to 17 different proteins with known function, 20.7% were homologous to nine hypothetical proteins and the remaining 41.5% had no identifiable homology;these may be novel genes. Two enzymatic genes involved in taxol production were found. The data presented in this study provide the first primary overview of a set of genes that are differentially expressed in N. sylviforme during taxol biosynthesis and form a solid foundation for the construction of high taxol-yielding genetically engineered strains.

关键词： endophytic fungus expressed sequence tag differentially expressed genes taxol biosynthetic pathway basic local alignment search tool

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Analysis of Polygala tenuifolia Transcriptome and Description of Secondary Metabolite Biosynthetic Pathways by Illumina Sequencing

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INTERNATIONAL JOURNAL OF GENOMICS 2015年第1期2015卷 782635-782635页

作者： Tian, Hongling Xu, Xiaoshuang Zhang, Fusheng Wang, Yaoqin Guo, Shuhong Qin, Xuemei Du, Guanhua Shanxi Acad Agr Sci Res Inst Econ Crop Fenyang 032200 Shanxi Peoples R China Shanxi Univ Modern Res Ctr Tradit Chinese Med Taiyuan 030006 Shanxi Peoples R China Shanxi Univ Coll Chem & Chem Engn Taiyuan 030006 Shanxi Peoples R China Chinese Acad Med Sci Inst Mat Med Beijing 100050 Peoples R China

Radix polygalae, the dried roots of Polygala tenuifolia and P. sibirica, is one of the most well-known traditional Chinese medicinal plants. Radix polygalae contains various saponins, xanthones, and oligosaccharide esters and these compounds are responsible for several pharmacological properties. To provide basic breeding information, enhance molecular biological analysis, and determine secondary metabolite biosynthetic pathways of P. tenuifolia, we applied Illumina sequencing technology and de novo assembly. We also applied this technique to gain an overview of P. tenuifolia transcriptome from samples with different years. Using Illumina sequencing, approximately 67.2% of unique sequences were annotated by basic local alignment search tool similarity searches against public sequence databases. We classified the annotated unigenes by using Nr, Nt, GO, COG, and KEGG databases compared with NCBI. We also obtained many candidates CYP450s and UGTs by the analysis of genes in the secondary metabolite biosynthetic pathways, including putative terpenoid backbone and phenylpropanoid biosynthesis pathway. With this transcriptome sequencing, future genetic and genomics studies related to the molecular mechanisms associated with the chemical composition of P. tenuifolia may be improved. Genes involved in the enrichment of secondary metabolite biosynthesis-related pathways could enhance the potential applications of P. tenuifolia in pharmaceutical industries.

关键词： basic local alignment search tool Transcriptome Sequencing Genes sequential data base metabolites Biosynthetic Pathways Pharmaceutical Industry unique sequences Polygala tenuifolia Analyses, Sequence biological analysis

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The Relationship Between Blast-related Hearing Threshold Shift and Insomnia in US Military Personnel

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MILITARY MEDICINE 2021年第9-10期186卷 844-849页

作者： MacGregor, Andrew J. Joseph, Antony R. Markwald, Rachel R. Dougherty, Amber L. Naval Hlth Res Ctr Med Modeling Simulat & Mission Support Dept San Diego CA 92106 USA Illinois State Univ Commun Sci & Disorders Dept Hearing Loss Prevent Lab Normal IL 61790 USA Leidos Inc San Diego CA 92106 USA Naval Hlth Res Ctr Warfighter Performance Dept San Diego CA 92106 USA

Introduction: Hearing loss and insomnia emerged as preeminent sources of morbidity among military service members and veterans who served in the recent Iraq and Afghanistan conflicts. Significant threshold shift (STS), an early indicator of hearing loss, has not been studied in relation to insomnia. This study's objective was to examine the co-occurrence of STS and insomnia among U.S. military personnel with blast-related injury. Materials and Methods: A total of 652 service members who were blast-injured during military operations in Iraq or Afghanistan between 2004 and 2012 were identified from the Blast-Related Auditory Injury Database. Pre- and post-injury audiometric data were used to ascertain new-onset STS, defined as 30 dB or greater increase for the sum of thresholds at 2,000, 3,000, and 4,000 Hz for either ear. Insomnia diagnosed within 2 years post-injury was abstracted from electronic medical records. Multivariable logistic regression analysis examined the relationship between STS and insomnia, while adjusting for age, year of injury, occupation, injury severity, tinnitus and concussion diagnosed in-theater, and PTSD. Results: A majority of the study sample was aged 18-25 years (79.9%) and sustained mild-to-moderate injuries (92.2%). STS was present in 21.1% of service members. Cumulative incidence of diagnosed insomnia was 22.3% and 11.1% for those with and without STS, respectively. After adjusting for covariates, those with STS had nearly 2-times higher odds of insomnia (odds ratio (OR)=1.91, 95% CI=1.12-3.24) compared with those without STS. In multivariable modeling, the strongest association was between PTSD and insomnia (OR=5.57, 95% CI=3.35-9.26). A secondary finding of note was that military personnel with STS had a significantly higher frequency of PTSD compared with those without STS (28.1% vs. 15.2%). Conclusions: Hearing threshold shift was associated with insomnia in military personnel with blast-related injury and could be used to identify

关键词： afghanistan brain concussion iraq military personnel post-traumatic stress disorder tinnitus insomnia hearing loss basic local alignment search tool

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AbGRI4, a novel antibiotic resistance island in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates

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JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY 2020年第10期75卷 2760-2768页

作者： Chan, Agnes P. Choi, Yongwook Clarke, Thomas H. Brinkac, Lauren M. White, Richard C. Jacobs, Michael R. Bonomo, Robert A. Adams, Mark D. Fouts, Derrick E. J Craig Venter Inst Rockville MD 20850 USA Case Western Reserve Univ Univ Hosp Cleveland Dept Pathol Med Ctr Cleveland OH 44106 USA Case Western Reserve Univ Dept Pathol Cleveland OH 44106 USA Case Western Reserve Univ Sch Med Dept Med Cleveland OH 44106 USA Louis Stokes Cleveland Dept Vet Affairs Med Ctr Cleveland OH USA Case Western Reserve Univ Sch Med Dept Mol Biol & Microbiol Cleveland OH 44106 USA Case Western Reserve Univ Sch Med Dept Pharmacol Cleveland OH 44106 USA Case Western Reserve Univ Sch Med Dept Biochem Cleveland OH 44106 USA Case Western Reserve Univ Sch Med Dept Prote & Bioinformat Cleveland OH USA CWRU Cleveland VAMC Ctr Antimicrobial Resistance Cleveland OH USA Jackson Lab Genom Med Farmington CT USA Translat Genom Res Inst Phoenix AZ USA Noblis Reston VA USA Booz Allen Hamilton Bethesda MD USA

Objectives: To investigate the genomic context of a novel resistance island (RI) in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates and global isolates. Methods: Using a combination of long and short reads generated from the Oxford Nanopore and Illumina platforms, contiguous chromosomes and plasmid sequences were determined. BLAST-based analysis was used to identify the RI insertion target. Results: Genomes of four multiply antibiotic-resistant A. baumannii clinical strains, from a US hospital system, belonging to prevalent MLST ST2 (Pasteur scheme) and ST281 (Oxford scheme) clade F isolates were sequenced to completion. A class 1 integron carrying aadB (tobramycin resistance) and aadA2 (streptomycin/spectinomycin resistance) was identified. The class 1 integron was 6.8kb, bounded by IS26 at both ends, and embedded in a new target location between an alpha/beta-hydrolase and a reductase. Due to its novel insertion site and unique RI composition, we suggest naming this novel RI AbGRI4. Molecular analysis of global A. baumannii isolates identified multiple AbGRI4 RI variants in non-ST2 clonal lineages, including variations in the resistance gene cassettes, integron backbone and insertion breakpoints at the hydrolase gene. Conclusions: A novel RI insertion target harbouring a class 1 integron was identified in a subgroup of ST2/ST281 clinical isolates. Variants of the RI suggested evolution and horizontal transfer of the RI across clonal lineages. Long- and short-read hybrid assembly technology completely resolved the genomic context of IS-bounded RIs, which was not possible using short reads alone.

关键词： plasmids antibiotic resistance bacterial chromosomes genes genome hydrolase oxidoreductase spectinomycin streptomycin tobramycin acinetobacter baumannii integrons naming function transfer technique resistance genes basic local alignment search tool il1rl1 gene

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The robustness of the chaos game representation to mutations and its application in free-alignment methods

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GENOMICS 2021年第3期113卷 1428-1437页

作者： Kania, Adrian Sarapata, Krzysztof Jagiellonian Univ Fac Biochem Biophys & Biotechnol Dept Computat Biophys & Bioinformat Gronostajowa 7 PL-30387 Krakow Poland

Numerical representation of biological sequences plays an important role in bioinformatics and has many practical applications. One of the most popular approaches is the chaos game representation. In this paper, the authors propose a novel look into chaos game construction - an analytical description of this procedure. This type enables to build more general number sequences using different weight functions. The authors suggest three conditions that these functions should hold. Additionally, they present some criteria to compare them and check whether they provide a unique representation. One of the most important advantages of our approach is the possibility to construct such a description that is less sensitive to mutations and as a result, give more reliable values for free-alignment phylogenetic trees constructions. Finally, the authors applied the DFT method using four types of functions and compared the obtained results using the BLAST tool.

关键词： Chaos game representation Free-alignment methods Phylogenetics Discrete Fourier transform Unweighted Pair Group Method with Arithmetic Mean basic local alignment search tool

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Screening of Lactobacillus isolates from gastrointestinal tract of guinea fowl for probiotic qualities using in vitro tests to select species-specific probiotic candidates

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BRITISH POULTRY SCIENCE 2016年第4期57卷 474-482页

作者： Vineetha, P. G. Tomar, S. Saxena, V. K. Susan, C. Sandeep, S. Adil, K. Mukesh, K. Div Avian Genet & Breeding Utarpradesh India Indian Vet Res Inst Div Vet Pathol Utarpradesh India Cent Avian Res Inst Poultry Econ & Agribusiness Res & Prioritizat Sec Utarpradesh India Cent Avian Res Inst Monitoring & Evaluat Sect Utarpradesh India CARI Avian Biotechnol Lab Div Avian Genet & Breeding Izatnagar Uttar Pradesh India

A total of 32 Lactobacillus isolates, 8 each from the crop (LGFCP1-LGFCP8), proventriculus (LGFP9-LGFP16), ileum (LGFI17-LGFI24) and caeca (LGFCM25-LGFCM32) were isolated from 25 adult guinea fowl (Pearl variety), 22-28weeks of age, and characterised morphologically, physiologically, biochemically and by molecular *** were screened for their probiotic quality using range of in vitro tests: aggregation test, cell surface hydrophobicity, resistance to bile salts and acidic conditions, enzymatic tests and coaggregation and antagonistic *** on in vitro test results and a novel scoring method, the two best isolates were selected and partial 16S rRNA sequencing was done. BLAST (basic local alignment search tool) analysis of sequence of isolate LGFCP4 showed 99% genetic identity with Lactobacillus plantarum and LGFP16 with Lactobacillus *** study shows that these two microbial agents may be suitable as potential probiotic candidates in guinea fowl, as well as in a feed supplement for other poultry species.

关键词： guineafowls basic local alignment search tool Bile Salts Lactobacillus plantarum in vitro test feed supplements Screening Gastrointestinal Tract Probiotics Lactobacillus

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