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PepBank - a database of peptides based on sequence text mining and public peptide data sources

BMC BIOINFORMATICS 2007年第1期8卷 1-10页

作者： Shtatland, Timur Guettler, Daniel Kossodo, Misha Pivovarov, Misha Weissleder, Ralph Harvard Univ Massachusetts Gen Hosp Sch Med Ctr Mol Imaging Res Charlestown MA 02129 USA No Essex Community Coll Haverhill MA 01830 USA

Background: Peptides are important molecules with diverse biological functions and biomedical uses. To date, there does not exist a single, searchable archive for peptide sequences or associated biological data. Rather, peptide sequences still have to be mined from abstracts and full-length articles, and/or obtained from the fragmented public sources. Description: We have constructed a new database (PepBank), which at the time of writing contains a total of 19,792 individual peptide entries. The database has a web-based user interface with a simple, Google-like search function, advanced text search, and BLAST and Smith-Waterman search capabilities. The major source of peptide sequence data comes from text mining of MEDLINE abstracts. Another component of the database is the peptide sequence data from public sources (ASPD and UniProt). An additional, smaller part of the database is manually curated from sets of full text articles and text mining results. We show the utility of the database in different examples of affinity ligand discovery. Conclusion: We have created and maintain a database of peptide sequences. The database has biological and medical applications, for example, to predict the binding partners of biologically interesting peptides, to develop peptide based therapeutic or diagnostic agents, or to predict molecular targets or binding specificities of peptides resulting from phage display selection. The database is freely available on http://***/, and the text mining source code (Peptide:: Pubmed) is freely available above as well as on CPAN (http://***/).

关键词： Peptide Sequence Text Mining basic local alignment search tool Phage Display Sequence Similarity search

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Biochemical characterization of a truncated β-agarase from Microbulbifer sp. suitable for efficient production of neoagarotetraose

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Process Biochemistry 2019年 87卷 119-127页

作者： Junwen Ma Qiaojuan Yan Ping Yi Shaoqing Yang Haijie Liu Zhengqiang Jiang Beijing Advanced Innovation Center for Food Nutrition and Human Health College of Engineering China Agricultural University No.17 Qinghua East Road Haidian District Beijing 100083 China College of Food Science and Nutritional Engineering China Agricultural University No.17 Qinghua East Road Haidian District Beijing 100083 China

A truncated β-agarase gene without the Carbohydrate-binding Modules (Aga16A-△CBM) from a marine bacterium Microbulbifer sp. BH-1 was cloned and successfully expressed in Escherichia coli . It encoded 279 amino acid (aa) with a predicted molecular mass of 42.1 kDa. The recombinant β-agarase (Aga16A-△CBM) showed the highest sequence identity of 49% with the glycoside hydrolase (GH) family 16 β-agarases AgaA and AgaB from Zobellia galactanivorans . Aga16A-△CBM showed optimal activity at 55°C and pH 8.0, respectively. It was stable within the pH range of 5.0–9.5 and up to 50°C. K m and V max values of Aga16A-△CBM for agarose were 1.32 mg ml −1 and 860.9 μmol min −1 mg −1 , respectively. In additional, agarose was hydrolyzed by Aga16A-△CBM to produce 18.4 mg mL −1 neoagarotetraose with the high yield of 93.2% (w/w). These desirable properties of Aga16A-△CBM may make it attractive in neoagarotetraose production.

关键词： GH glycoside hydrolase CBM Carbohydrate-Binding Modules AOS agaro-oligosaccharides NAOS neoagaro-oligosaccharides DNA deoxyribonucleic PCR polymerase chain reaction TAIL-PCR Thermal Asymmetric Interlaced PCR CBM Carbohydrate-binding Modules BLAST basic local alignment search tool ORF open reading frame IPTG Isopropyl-β-D-galactopyranoside LB Luria−Bertani NTA nitrilotriacetic acid SDS sodium dodecyl sulfate PAGE polyacrylamide gel electrophoresis DNS 3,5-dinitrosalicylic acid EDTA ethylene diamine tetraacetic TLC thin layer chromatography HPLC high-performance liquid chromatography NA2 neoagarobiose NA4 neoagarotetraose NA6 neoagarohexaose NA8 neoagarooctaose Microbulbifer sp. β-agarase Characterization Neoagarotetraose

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RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags

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BMC BIOINFORMATICS 2011年第s10期12卷 S20-S20页

作者： Li, Ying Gong, Ping Perkins, Edward J. Zhang, Chaoyang Wang, Nan SpecPro Inc Environm Serv San Antonio TX 78216 USA Univ So Mississippi Sch Comp Hattiesburg MS 39406 USA USA Environm Lab Engineer Res & Dev Ctr Vicksburg MS 39180 USA

Background: Gene Regulatory Networks (GRNs) provide integrated views of gene interactions that control biological processes. Many public databases contain biological interactions extracted from experimentally validated literature reports, but most furnish only information for a few genetic model organisms. In order to provide a bioinformatic tool for researchers who work with non-model organisms, we developed RefNetBuilder, a new platform that allows construction of putative reference pathways or GRNs from expressed sequence tags (ESTs). Results: RefNetBuilder was designed to have the flexibility to extract and archive pathway or GRN information from public databases such as the Kyoto Encyclopedia of Genes and Genomes (KEGG). It features sequence alignment tools such as BLAST to allow mapping ESTs to pathways and GRNs in model organisms. A scoring algorithm was incorporated to rank and select the best match for each query EST. We validated RefNetBuilder using DNA sequences of Caenorhabditis elegans, a model organism having manually curated KEGG pathways. Using the earthworm Eisenia fetida as an example, we demonstrated the functionalities and features of RefNetBuilder. Conclusions: The RefNetBuilder provides a standalone application for building reference GRNs for non-model organisms on a number of operating system platforms with standard desktop computer hardware. As a new bioinformatic tool aimed for constructing putative GRNs for non-model organisms that have only ESTs available, RefNetBuilder is especially useful to explore pathway-or network-related information in these organisms.

关键词： Query Sequence basic local alignment search tool Boolean Network KEGG Orthology Probabilistic Boolean Network

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Identification of Specific Markers Linked to Regional Differentiation ofWarburgia ugandensis

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Journal of Life Sciences 2013年第1期5卷 29-40页

Warburgia ugandensisis an important African medicinal tree. The species population has shown a high genetic differentiation in the Kenya’s Rift Valley. Nine populations were analysed by Bulk Segregant Analysis employing Random Amplified Polymorphic DNA marker technique to identify regional differentiation-linked markers within and across Kenyan Rift Valley. Five primers showed putative East and West genetic differentiation. Diagnostic markers were isolated, cloned, sequenced and compared with Genbank sequences using BLAST algorithms. Three, (WarburgiaIC15E, WarburgiaIC55EandWarburgiaIC28W) sequences showed homology to plant and bacterial-like chromosomal sequences with low E-values. Sequence alignment indicated conserved protein domains of plants and bacteria-like sequences. Phylogenetic analysis revealed high rates of genetic distances (H” 0.8) and a low rate of disparity indices of (0), suggesting some evolutionary forces behind demographic differentiation. These imply that genetic differentiation observed might be due to genetic mutants in certain domains of chromosome that may have some implication on genome functionality.

关键词： Random Amplified Polymorphic DNA Amplified Fragment Length Polymorphism basic local alignment search tool Multiple Sequence alignment Sequence

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Genome comparison of two Coccolithoviruses

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VIROLOGY JOURNAL 2006年第0期3卷 15-15页

作者： Allen, Michael J. Schroeder, Declan C. Donkin, Andrew Crawfurd, Katharine J. Wilson, William H. Plymouth Marine Lab Plymouth PL1 3DH Devon England Marine Biol Assoc UK Plymouth PL1 2PB Devon England

Background: The Coccolithoviridae is a recently discovered family of viruses that infect the marine coccolithophorid Emiliania huxleyi. Following on from the sequencing of the type strain EhV-86, we have sequenced a second strain, EhV-163. Results: We have sequenced approximately 80% of the EhV-163 genome, equating to more than 200 full length CDSs. Conserved and variable CDSs and a gene replacement have been identified in the EhV-86 and EhV-163 genomes. Conclusion: The sequencing of EhV-163 has provided a wealth of information which will aid the re-annotating of the EhV-86 genome and identified a gene insertion in EhV-163.

关键词： basic local alignment search tool Homing Endonuclease High Selection Pressure Algal Virus Putative Membrane Protein

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Detection of Balamuthia mandrillaris DNA by real-time PCR targeting the RNase P gene

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BMC MICROBIOLOGY 2008年第1期8卷 210-210页

作者： Kiderlen, Albrecht F. Radam, Elke Lewin, Astrid Robert Koch Inst Cellular Immunol Unit P22 D-13353 Berlin Germany

Background: The free-living amoeba Balamuthia mandrillaris may cause fatal encephalitis both in immunocompromised and in - apparently - immunocompetent humans and other mammalian species. Rapid, specific, sensitive, and reliable detection requiring little pathogen-specific expertise is an absolute prerequisite for a successful therapy and a welcome tool for both experimental and epidemiological research. Results: A real-time polymerase chain reaction assay using TaqMan (R) probes (real-time PCR) was established specifically targeting the RNase P gene of B. mandrillaris amoebae. The assay detected at least 2 (down to 0.5) genomes of B. mandrillaris grown in axenic culture. It did not react with DNA from closely related Acanthamoeba (3 species), nor with DNA from Toxoplasma gondii, Leishmania major, Pneumocystis murina, Mycobacterium bovis (BCG), human brain, various mouse organs, or from human and murine cell lines. The assay efficiently detected B. mandrillaris DNA in spiked cell cultures, spiked murine organ homogenates, B. mandrillaris-infected mice, and CNS tissue-DNA preparations from 2 patients with proven cerebral balamuthiasis. This novel primer set was successfully combined with a published set that targets the B. mandrillaris 18S rRNA gene in a duplex real-time PCR assay to ensure maximum specificity and as a precaution against false negative results. Conclusion: A real-time PCR assay for B. mandrillaris amoebae is presented, that is highly specific, sensitive, and reliable and thus suited both for diagnosis and for research.

关键词： basic local alignment search tool Mycobacterium Bovis basic local alignment search tool Analysis Granulomatous Amebic Encephalitis Granulomatous Amebic Encephalitis

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RGD v2.0: a major update of the ruminant functional and evolutionary genomics database

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NUCLEIC ACIDS REsearch 2022年第D1期50卷 D1091-D1099页

作者： Fu, Weiwei Wang, Rui Nanaei, Hojjat Asadollahpour Wang, Jinxin Hu, Dexiang Jiang, Yu Northwest A&F Univ Key Lab Anim Genet Breeding & Reprod Shaanxi Prov Coll Anim Sci & Technol Yangling 712100 Shaanxi Peoples R China Northwest A&F Univ Ctr Ruminant Genet & Evolut Yangling 712100 Shaanxi Peoples R China

Ruminant Genome Database (RGD;http://***/RGD) provides visualization and analysis tools for ruminant comparative genomics and functional annotations. As more high-quality ruminant genome assemblies have become available, we have redesigned the user interface, integrated and expanded multi-omics data, and developed novel features to improve the database. The new version, RGD v2.0, houses 78 ruminant genomes;110-species synteny alignments for major livestock (including cattle, sheep, goat) and wild ungulates;21 012 orthologous gene clusters with Gene Ontology and pathway annotation;similar to 8 600 000 conserved elements;and similar to 1 000 000 cis-regulatory elements by utilizing 1053 epigenomic data sets. The transcriptome data in RGD v2.0 has nearly doubled, currently with 1936 RNA-seq data sets, and 155 174 phenotypic data sets have been newly added. New and updated features include: (i) The UCSC Genome Browser, BLAT, BLAST and Table Browser tools were updated for six available ruminant livestock species. (ii) The LiftOver tool was newly introduced into our browser to allow coordinate conversion between different ruminant assemblies. And (iii) tissue specificity index, tau, was calculated to facilitate batch screening of specifically expressed genes. The enhanced genome annotations and improved functionality in RGD v2.0 will be useful for study of genome evolution, environmental adaption, livestock breeding and biomedicine.

关键词： phenotype breeding cattle genes genome genomics ruminants sheep synteny tau proteins farm animals galveston orientation and amnesia test basic local alignment search tool datasets epigenomics rna-seq

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Genomic sequencing and analysis of a Chinese hamster ovary cell line using Illumina sequencing technology

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BMC GENOMICS 2011年第1期12卷 67-67页

作者： Hammond, Stephanie Swanberg, Jeffrey C. Kaplarevic, Mihailo Lee, Kelvin H. Univ Delaware Dept Chem Engn Newark DE 19711 USA Univ Delaware Delaware Biotechnol Inst Newark DE 19711 USA

Background: Chinese hamster ovary (CHO) cells are among the most widely used hosts for therapeutic protein production. Yet few genomic resources are available to aid in engineering high-producing cell lines. Results: High-throughput Illumina sequencing was used to generate a 1x genomic coverage of an engineered CHO cell line expressing secreted alkaline phosphatase (SEAP). Reference-guided alignment and assembly produced 3.57 million contigs and CHO-specific sequence information for similar to 18,000 mouse and similar to 19,000 rat orthologous genes. The majority of these genes are involved in metabolic processes, cellular signaling, and transport and represent attractive targets for cell line engineering. Conclusions: This demonstrates the applicability of next-generation sequencing technology and comparative genomic analysis in the development of CHO genomic resources.

关键词： Chinese Hamster Ovary Cell Chinese Hamster Ovary basic local alignment search tool Bacterial Artificial Chromosome Library Chinese Hamster Ovary Cell Line

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The zebrafish genome encodes the largest vertebrate repertoire of functional aquaporins with dual paralogy and substrate specificities similar to mammals

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BMC EVOLUTIONARY BIOLOGY 2010年第1期10卷 38-38页

作者： Tingaud-Sequeira, Angele Calusinska, Magdalena Finn, Roderick N. Chauvigne, Francois Lozano, Juanjo Cerda, Joan CSIC Lab Inst Recerca & Tecnol Agroalimentaries Inst Ciencias Mar E-08003 Barcelona Spain Univ Bordeaux 1 UMR NuAGe F-33405 Talence France Univ Liege Ctr Prot Engn B-4000 Liege Belgium Univ Bergen Dept Biol Bergen High Technol Ctr N-5020 Bergen Norway CIBERehd Barcelona 08036 Spain

Background: Aquaporins are integral membrane proteins that facilitate the transport of water and small solutes across cell membranes. These proteins are vital for maintaining water homeostasis in living organisms. In mammals, thirteen aquaporins (AQP0-12) have been characterized, but in lower vertebrates, such as fish, the diversity, structure and substrate specificity of these membrane channel proteins are largely unknown. Results: The screening and isolation of transcripts from the zebrafish ( Danio rerio) genome revealed eighteen sequences structurally related to the four subfamilies of tetrapod aquaporins, i.e., aquaporins (AQP0, -1 and -4), water and glycerol transporters or aquaglyceroporins (Glps;AQP3 and AQP7-10), a water and urea transporter (AQP8), and two unorthodox aquaporins (AQP11 and -12). Phylogenetic analyses of nucleotide and deduced amino acid sequences demonstrated dual paralogy between teleost and human aquaporins. Three of the duplicated zebrafish isoforms have unlinked loci, two have linked loci, while DrAqp8 was found in triplicate across two chromosomes. Genomic sequencing, structural analysis, and maximum likelihood reconstruction, further revealed the presence of a putative pseudogene that displays hybrid exons similar to tetrapod AQP5 and -1. Ectopic expression of the cloned transcripts in Xenopus laevis oocytes demonstrated that zebrafish aquaporins and Glps transport water or water, glycerol and urea, respectively, whereas DrAqp11b and -12 were not functional in oocytes. Contrary to humans and some rodents, intrachromosomal duplicates of zebrafish AQP8 were water and urea permeable, while the genomic duplicate only transported water. All aquaporin transcripts were expressed in adult tissues and found to have divergent expression patterns. In some tissues, however, redundant expression of transcripts encoding two duplicated paralogs seems to occur. Conclusion: The zebrafish genome encodes the largest repertoire of functional vertebrate a

关键词： basic local alignment search tool Whole Genome Duplication Zebrafish Genome Aquaporin Gene Redundant Expression

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A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata)

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BMC GENOMICS 2010年第1期11卷 218-218页

作者： Ball, Alexander D. Stapley, Jessica Dawson, Deborah A. Birkhead, Tim R. Burke, Terry Slate, Jon Univ Sheffield Dept Anim & Plant Sci Sheffield S10 2TN S Yorkshire England

Background: Genetic linkage maps are essential tools when searching for quantitative trait loci (QTL). To maximize genome coverage and provide an evenly spaced marker distribution a combination of different types of genetic marker are sometimes used. In this study we created linkage maps of four zebra finch (Taeniopygia guttata) chromosomes (1, 1A, 2 and 9) using two types of marker, Single Nucleotide Polymorphisms (SNPs) and microsatellites. To assess the effectiveness and accuracy of each kind of marker we compared maps built with each marker type separately and with both types of marker combined. Linkage map marker order was validated by making comparisons to the assembled zebra finch genome sequence. Results: We showed that marker order was less reliable and linkage map lengths were inflated for microsatellite maps relative to SNP maps, apparently due to differing error rates between the two types of marker. Guidelines on how to minimise the effects of error are provided. In particular, we show that when combining both types of marker the conventional process of building linkage maps, whereby the most informative markers are added to the map first, has to be modified in order to improve map accuracy. Conclusions: When using multiple types and large numbers of markers to create dense linkage maps, the least error prone loci (SNPs) rather than the most informative should be used to create framework maps before the addition of other potentially more error prone markers (microsatellites). This raises questions about the accuracy of marker order and predicted recombination rates in previous microsatellite linkage maps which were created using the conventional building process, however, provided suitable error detection strategies are followed microsatellite-based maps can continue to be regarded as reasonably reliable.

关键词： Linkage Group basic local alignment search tool Zebra Finch Marker Order Genotyping Error Rate

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