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Extracting protein alignment models from the sequence database

NUCLEIC ACIDS RESEARCH 1997年第9期25卷 1665-1677页

作者： Neuwald, AF Liu, JS Lipman, DJ Lawrence, CE STANFORD UNIV DEPT STAT STANFORD CA 94305 USA NEW YORK STATE DEPT HLTH WADSWORTH CTR LABS & RES BIOMETR LAB ALBANY NY 12201 USA

Biologists often gain structural and functional insights into a protein sequence by constructing a multiple alignment model of the family. Here a program called PROBE fully automates this process of model construction starting from a single sequence. Central to this program is a powerful new method to locate and align only those, often subtly, conserved patterns essential to the family as a whole. When applied to randomly chosen proteins, PROBE found on average about four times as many relationships as a pairwise search and yielded many new discoveries, These include: an obscure subfamily of globins in the roundworm Caenorhabditis elegans;two new superfamilies of metallohydrolases;a lipoyl/biotin swinging arm domain in bacterial membrane fusion proteins;and a DH domain in the yeast Bud3 and Fus2 proteins. By identifying distant relationships and merging families into superfamilies in this way, this analysis further confirms the notion that proteins evolved from relatively few ancient sequences, Moreover, this method automatically generates models of these ancient conserved regions for rapid and sensitive screening of sequences.

关键词： .pairwise starting superfamilies distant constructing conserved regions sequence database globins alignment model single sequence conserved patterns

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Compact variant-rich customized sequence database and a fast and sensitive database search for efficient proteogenomic analyses

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PROTEOMICS 2014年第23-24期14卷 2742-2749页

作者： Park, Heejin Bae, Junwoo Kim, Hyunwoo Kim, Sangok Kim, Hokeun Mun, Dong-Gi Joh, Yoonsung Lee, Wonyeop Chae, Sehyun Lee, Sanghyuk Kim, Hark Kyun Hwang, Daehee Lee, Sang-Won Paek, Eunok Hanyang Univ Dept Comp Sci & Engn Seoul 133791 South Korea Ewha Womans Univ Dept Life Sci Seoul South Korea Ewha Womans Univ Ewha Res Ctr Syst Biol Seoul South Korea Korea Univ Dept Chem Res Inst Nat Sci Seoul 136701 South Korea DGIST Dept New Biol Taegu South Korea DGIST Ctr Plant Aging Res Inst Basic Sci Taegu South Korea Natl Canc Ctr Goyang South Korea

In proteogenomic analysis, construction of a compact, customized database from mRNA-seq data and a sensitive search of both reference and customized databases are essential to accurately determine protein abundances and structural variations at the protein level. However, these tasks have not been systematically explored, but rather performed in an ad-hoc fashion. Here, we present an effective method for constructing a compact database containing comprehensive sequences of sample-specific variantssingle nucleotide variants, insertions/deletions, and stop-codon mutations derived from Exome-seq and RNA-seq data. It, however, occupies less space by storing variant peptides, not variant proteins. We also present an efficient search method for both customized and reference databases. The separate searches of the two databases increase the search time, and a unified search is less sensitive to identify variant peptides due to the smaller size of the customized database, compared to the reference database, in the target-decoy setting. Our method searches the unified database once, but performs target-decoy validations separately. Experimental results show that our approach is as fast as the unified search and as sensitive as the separate searches. Our customized database includes mutation information in the headers of variant peptides, thereby facilitating the inspection of peptide-spectrum matches.

关键词： Bioinformatics Early onset gastric cancer Peptide identification Proteogenomics sequence database

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A sequence database analysis of 5-nitroimidazole reductase and related proteins to expand knowledge on enzymes responsible for metronidazole inactivation

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ANAEROBE 2019年 55卷 29-34页

作者： Alauzet, Corentine Aujoulat, Fabien Lozniewski, Alain Marchandin, Helene Univ Lorraine EA Stress Immunite Pathogenes SIMPA 7300 F-54000 Nancy France Univ Lorraine Lab Bacteriol CHRU Nancy F-54000 Nancy France Univ Montpellier CNRS HydroSci Montpellier IRD Montpellier France Univ Montpellier CHU Nimes CNRS Dept MicrobiolHydroSci MontpellierIRD Nimes France

nim genes are associated, in combination with other factors, with acquired resistance to metronidazole (MTZ) in anaerobes. These genes encode 5-nitroimidazole reductase enzymes (Nim proteins) that reduce MTZ into an inactive compound. Eleven variants (nimA to nimK) are currently described in anaerobes with either a chromosomal or a plasmidic location. Mostly found in members of the Bacteroides fragilis group, nim genes were demonstrated in anaerobic taxa outside the phylum Bacteroidetes. Nitroreductase enzymes, weakly related to those found in Bacteroidetes but associated with MTZ inactivation, were also characterized both in anaerobic and non-anaerobic taxa. Published data only poorly reflect the growing number of data from cultivation-independent studies and sequences deposited in databases. Considering this limitation, we performed herein an analysis of the sequence databases with the aim to increase the current knowledge on Nim protein distribution and diversity. The 250 sequences the most closely related to the 11 known Nim proteins were selected and analyzed for identity level and phylogenetic relationships with Nim A to K proteins. The analysis revealed a larger diversity of anaerobic species harboring known Nim proteins than that currently described in the literature. Putative new variants of known Nim proteins and novel Nim proteins were found. In addition, nitroreductase proteins and homologs related to the pyridoxamine 5'phosphate oxidase family were found in highly diverse anaerobic and aerobic taxa of human but also animal and environmental origin. On the other hand, we found a very low number of sequences recovered from metagenomic studies. Considering the different databases currently available to identify antimicrobial resistance genes (ARG) among metagenomic sequences, we hypothesized that this may, at least in part, be related to the incompleteness of ARG databases because none of them includes the 11 described nim genes at the time of our study. B

关键词： nim genes Diversity Distribution Nitroreductases Homologs sequence database

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U-insertion/deletion Edited sequence database

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NUCLEIC ACIDS RESEARCH 1998年第1期26卷 170-176页

作者： Simpson, L Wang, SH Thiemann, OH Alfonzo, JD Maslov, DA Avila, HA Univ Calif Los Angeles Howard Hughes Med Inst Los Angeles CA 90095 USA Univ Calif Los Angeles Dept Mol Cell & Dev Biol Los Angeles CA 90095 USA Univ Calif Los Angeles Sch Med Dept Immunol & Med Microbiol Los Angeles CA 90024 USA Univ Calif Riverside Dept Biol Riverside CA 92521 USA Univ Kentucky Med Ctr Dept Biochem Lexington KY 40536 USA

Uridine insertion/deletion RNA editing posttranscriptional RNA modification occurring in the mitochondria of kinetoplastid protozoa. The U-insertion/deletion Edited sequence database is a compilation of mitochondrial genes and edited mRNAs from five kinetoplastid species. It contains separate files with the DNA, mRNA (both unedited and edited) and predicted protein sequences, as well as alignments of the Leishmania tarentolae and Trypanosoma brucei protein sequences from edited and unedited genes, The sequence files are in GCG format. A 'map' sequence file showing the location of U-deletions, U-insertions and the translated amino acid sequences is also provided for each gene. Genomic maps for each species are also provided with clickable genes, including maxicircle-encoded gRNAs. Sets of aligned nuclear rRNA sequences from kinetoplastid protozoa are also provided, which were used for phylogenetic reconstructions in an analysis of the origin of RNA editing, The database is available through the World Wide Web as an HTML document at the URL http://***/RNA/trypanosome/***.

关键词： .CA USA protozoa Trypanosoma alignments sequence database Leishmania tarentolae kinetoplastid species unedited

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A Parallel Algorithm for Mining Non-Redundant Recurrent Rules from a sequence database

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JOURNAL OF ADVANCED COMPUTATIONAL INTELLIGENCE AND INTELLIGENT INFORMATICS 2019年第5期23卷 956-961页

作者： Yoon, Seung-Yong Seki, Hirohisa Nagoya Inst Technol Dept Comp Sci Showa Ku Gokiso Cho Nagoya Aichi 4668555 Japan

We propose a parallel algorithm for mining non-redundant recurrent rules from a sequence database. Recurrent rules, proposed by Lo et al. [1], can express "Whenever a series of precedent events occurs, eventually a series of consequent events occurs," and they have shown the usefulness of recurrent rules in various domains, including software specification and verification. Although some algorithms such as NR3 have been proposed, mining non-redundant recurrent rules still requires considerable processing time. To reduce the computation cost, we present a parallel approach to mining non-redundant recurrent rules, which fully utilizes the task-parallelism in NR3. We also give some experimental results, which show the effectiveness of our proposed method.

关键词： data mining sequential rule recurrent rule sequence database parallel algorithm

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Establishment of tyrosinase sequence database in normally pigmented Indians and Japanese for rapid determination of novel mutations

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JOURNAL OF DERMATOLOGICAL SCIENCE 2005年第3期39卷 167-173页

作者： Miyamura, Y Verma, IC Saxena, R Murase, A Kono, M Suzuki, T Yasue, S Shibata, S Sakakibara, A Tomita, Y Nagoya Univ Grad Sch Med Dept Dermatol Nagoya Aichi Japan Sir Ganga Ram Hosp Dept Med Genet New Delhi India

Background: Many mutations of the tyrosinase gene have been reported in oculocutaneous albinism type I (OCA1) patient. In the future, a greater number of novel mutations will be found as the search for pathological mutations in the tyrosinase genes of OCA patients from various ethnic origins. For rapid determination in future whether an observed mutation is a polymorphism or a novel pathological one, sequence databases of the gene of various ethnic people are needed. Objective: We established a sequence database of the tyrosinase gene of Japanese as well as Indian people. Method: We collected DNA from 109 Japanese and 103 Indians with normal pigmentation and analyzed their tyrosinase gene using a direct sequencing method. Result: The database shows an apparent difference between the two ethnic groups in polymorphisms of the tyrosinase gene namely, Q402 allele, Y192 allele and IV2 + 24 insT were found in the Indian population, but not in the Japanese. On the other hand, some Japanese had IV2-21 insT but none of the Indians did. The database supports the notion that the tyrosinase gene evolved and extended separately in the two ethnic groups. And the developing database confirmed that the reported mutations causing Indian and Japanese OCA were not among the polymorphisms in the database, which conversely gives genetical proof of the "genuine" pathological mutations. Conclusion: Eventually, the sequence database we established will contribute to demonstrating novel mutations of albinism in Indians and Japanese. (c) 2005 Japanese Society for Investigative Dermatology. Elsevier Ireland Ltd. All rights reserved.

关键词： tyrosinase OCA1 sequence database mutation ethnic difference polymorphisms

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TestisBank: an internet-based gene sequence database of the testis

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INTERNATIONAL JOURNAL OF ANDROLOGY 2002年第3期25卷 175-179页

作者： Claussen, S Prokosch, HU Nieschlag, E Gromoll, J Univ Munster Inst Reprod Med D-48129 Munster Germany Univ Munster Inst Med Informat & Biomath D-4400 Munster Germany

The testis is a highly transcriptionally active organ with hundreds of genes expressed during different stages of spermatogenesis. Scientists working on the testis are restricted to using two sources for further information on testicular genes, GenBank and MEDLINE. However, these two databases are not completely linked and give only very little information on the cellular type of expression or whether a gene is cloned in other tissues but is also expressed in the testis. We have generated an organ-specific database named TestisBank, which is capable of retrieving a more complete set of genes expressed in the different cell types of the testis. Furthermore, it extends to the epididymis which plays an important role in germ cell maturation. TestisBank is automatically updated to match the current status of sequence entries in the genome databases and it provides the user with an interface convenient to handle and provides useful links related to male reproduction. The TestisBank is publicly available at http://***/TestisBank/. The design of the TestisBank may provide a simple model for the development of databases in which molecular and literature data are merged, thereby allowing detailed insight into the contribution of different cells/genes to the complex process of spermatogenesis.

关键词： epididymis sequence database spermatogenesis testis database

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A sequence database allowing automated genotyping of Classical swine fever virus isolates

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JOURNAL OF VIROLOGICAL METHODS 2007年第1-2期140卷 95-99页

作者： Dreier, Sabrina Zimmermann, Bernd Moennig, Volker Greiser-Wilke, Irene Univ Vet Med Inst Virol Dept Infect Dis EU Reference Lab Class Swine Fever D-30559 Hannover Germany

Classical swine fever (CSF) is a highly contagious viral disease of pigs. According to the OIE classification of diseases it is classified as a notifiable (previously List A) disease, thus having the potential for causing severe socio-economic problems and affecting severely the international trade of pigs and pig products. Effective control measures are compulsory, and to expose weaknesses a reliable tracing of the spread of the virus is necessary. Genetic typing has proved to be the method of choice. However, genotyping involves the use of multiple software applications, which is laborious and complex. The implementation of a sequence database, which is accessible by the World Wide Web with the option to type automatically new CSF virus isolates once the sequence is available is described. The sequence to be typed is tested for correct orientation and, if necessary, adjusted to the right length. The alignment and the neighbor-joining phylogenetic analysis with a standard set of sequences can then be calculated. The results are displayed as a graph. As ail example, the determination is shown of the genetic subgroup of the isolate obtained from the outbreaks registered in Russia, in 2005. After registration (***-wilike @***) the database including the module for genotyping are accessible under http://***-haiinovei-.de/eg/***. (c) 2006 Elsevier B.V. All rights reserved.

关键词： classical swine fever virus sequence database genetic typing automation

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The EMBL nucleotide sequence database

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NUCLEIC ACIDS RESEARCH 2001年第1期29卷 17-21页

作者： Stoesser, G Baker, W van den Broek, A Camon, E Garcia-Pastor, M Kanz, C Kulikova, T Lombard, V Lopez, R Parkinson, H Redaschi, N Sterk, P Stoehr, P Tuli, MA EMBL Outstn European Bioinformat Inst Cambridge CB10 1SD England

The EMBL Nucleotide sequence database (http:// ***/embI/) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank at the NCBI (USA). Data is exchanged amongst the collaborating databases on a daily basis. The major contributors to the EMBL database are individual authors and genome project groups. Webin is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from targe-scale genome sequencing centres and from the European Patent Office (EPO). database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via ftp, email and World Wide Web interfaces, EBI's sequence Retrieval System (SRS), a network browser for databanks in molecular biology, integrates and links the main nucleotide and protein databases plus many specialized databases. For sequence similarity searching a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide sequence database and SWISS-PROT.

关键词： .GenBank email EMBL database EPO genome sequencing genome project submission sequence database DDBJ submitters

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Histone sequence database: new histone fold family members

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NUCLEIC ACIDS RESEARCH 1998年第1期26卷 372-375页

作者： Baxevanis, AD Landsman, D NIH Natl Ctr Biotechnol Informat Natl Lib Med Bethesda MD 20894 USA NIH Genome Technol Branch Natl Ctr Human Genome Res Bethesda MD 20892 USA

Searches of the major public protein databases with core and linker chicken and human histone sequences have resulted in the compilation of an annotated set of histone protein sequences, In addition, new database searches with two distinct motif search algorithms have identified several members of the histone fold family, including human DRAP1 and yeast CSE4. database resources include information on conflicts between similar sequence entries in different source databases, multiple sequence alignments, links to the Entrez integrated information retrieval system, structures for histone and histone fold proteins, and the ability to visualize structural data through Cn3D. The database currently contains >1000 protein sequences, which are searchable by protein type, accession number, organism name, or any other free text appearing in the definition line of the entry, All sequences and alignments in this database are available through the World Wide Web at http://***/DIR/GTB/HISTONES or http://***/Baxevani/HISTONES.

关键词： .protein sequences Family Members conflicts alignments searches sequence database sequence entries new histone Histone Fold Motif motif search DRAP

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