{"title":"On the Structure of Reconciliations","authors":"P. Górecki, J. Tiuryn","doi":"10.1007/978-3-540-32290-0_4","DOIUrl":"https://doi.org/10.1007/978-3-540-32290-0_4","url":null,"abstract":"","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2004-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89291427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Identifying Evolutionarily Conserved Segments Among Multiple Divergent and Rearranged Genomes","authors":"B. Mau, A. Darling, N. Perna","doi":"10.1007/978-3-540-32290-0_6","DOIUrl":"https://doi.org/10.1007/978-3-540-32290-0_6","url":null,"abstract":"","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2004-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76225479","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The Statistical Significance of Max-Gap Clusters","authors":"Rose Hoberman, D. Sankoff, D. Durand","doi":"10.1007/978-3-540-32290-0_5","DOIUrl":"https://doi.org/10.1007/978-3-540-32290-0_5","url":null,"abstract":"","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2004-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83015854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Toward a Phylogenetically Aware Algorithm for Fast DNA Similarity Search","authors":"J. Buhler, Rachel K. Nordgren","doi":"10.1007/978-3-540-32290-0_2","DOIUrl":"https://doi.org/10.1007/978-3-540-32290-0_2","url":null,"abstract":"","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2004-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76618679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Stemming the tide of genomics: computational genomics III.","authors":"C L Carter, A R Kerlavage","doi":"10.1089/10906590050145212","DOIUrl":"https://doi.org/10.1089/10906590050145212","url":null,"abstract":"THE GENOME REVOLUTION IS HERE. This revolution is unlocking the secrets of the entire DNA sequence of many microorganisms, beginning with Haemophilus influenza, some plants, and soon, the genome of the human will be revealed in its complete, annotated form. The effort has been likened to viewing the surface of a new planet for the first time. The information buried in the genes of a variety of living creatures will be used, in part, to trace human origins and to uncover clues to human diseases. Fortunately, the science of bioinformatics has kept pace with this explosion of data and provides us with the tools needed to analyze and interpret a vast amount of sequence information. Computer software programs containing elaborate algorithms to assemble and annotate genomic sequences, to identify coding regions, and to search for homologies are now widely used. Increasingly, there is an effort to reduce, as much as possible, the human intervention needed in both the collection and the editing of data. As the field matures, software programs for DNA sequencing and assembly will address new challenges including gene characterizations, comparative analyses of human and nonhuman genomic sequences, protein structure and function, and will contribute to the identification of target proteins for drug design. A new generation of tools combine computational methods with experimental technologies. The Third Annual Conference on Computational Genomics was held November 18–21, 1999 at the Renaissance Harborplace Hotel in Baltimore, MD. This year’s conference was organized by Anthony R. Kerlavage of Celera Genomics, Steven Salzberg of The Institute for Genomic Research (TIGR), and David Searls of SmithKline Beecham Pharmaceuticals.","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/10906590050145212","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21844604","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Molecular cloning of the Atlantic cod chymotrypsinogen B.","authors":"R Spilliaert, A Gudmundsdóttir","doi":"10.1089/10906590050145258","DOIUrl":"https://doi.org/10.1089/10906590050145258","url":null,"abstract":"<p><p>The cDNA encoding Atlantic cod (Gadus morhua) chymotrypsinogen B has been isolated and sequenced. Its deduced amino acid sequence consists of a 16-residue signal sequence and a mature polypeptide of 247 residues, being two residues longer than its vertebrate analogs. This mature polypeptide corresponds to a calculated molecular mass of 26.5 kDa and shares 70% sequence identity with cod chymotrypsinogen A. However, the identity between cod chymotrypsinogen B and its other vertebrate analogues is 63-66%. In common with most fish serine proteases, cod chymotrypsinogen B contains a high number of methionine residues. The presence of a threonine instead of a highly conserved serine residue at position 189 is a novel characteristic of this enzyme. Cod chymotrypsin B, as its type B vertebrate analogs, has an alanine at position 226, whereas a glycine is most commonly found at this position in the type A chymotrypsins.</p>","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/10906590050145258","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21845087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
R. Hernández-Castro, A. Verdugo-Rodríguez, J. A. Gutiérrez-Pabello, L. G. Adams, F. Suárez-Güemes, A. Sahagún-Ruiz
{"title":"Identification of four genes of the Brucella melitensis ATP synthase operon F0 sector: relationship with the Rhodospirillaceae family.","authors":"R. Hernández-Castro, A. Verdugo-Rodríguez, J. A. Gutiérrez-Pabello, L. G. Adams, F. Suárez-Güemes, A. Sahagún-Ruiz","doi":"10.1089/OMI.1.2000.5.163","DOIUrl":"https://doi.org/10.1089/OMI.1.2000.5.163","url":null,"abstract":"We have determined the nucleotide sequence of a cloned DNA fragment from the human and animal pathogen Brucella melitensis. Four genes were identified from a 4069 bp fragment, corresponding to the B. melitensis a, c, b', and b subunits of the ATP synthase F0 sector operon. A duplicated and divergent copy of the b-subunit gene was observed. This feature has been found only in photosynthetic bacteria and chloroplasts. In addition, the gene cluster was separated from the F1 sector, a characteristic described only for the Rhodospirillaceae family.","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/OMI.1.2000.5.163","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60513841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
F. Sangari, Magi Bächli, Luiz E. Bermudez, Thomas Bodmer
{"title":"Characterization of IS666, a newly described insertion element of Mycobacterium avium.","authors":"F. Sangari, Magi Bächli, Luiz E. Bermudez, Thomas Bodmer","doi":"10.1089/OMI.1.2000.5.181","DOIUrl":"https://doi.org/10.1089/OMI.1.2000.5.181","url":null,"abstract":"The insertion sequence IS666 was isolated from Mycobacterium avium strain 101. IS666 is a 1474 bp insertion sequence belonging to the IS256 family, that includes IS6120 from Mycobacterium smegmatis, IS1166 and IS1295 from Rhodococcus sp. IGTS8, IST2 from Thiobacillus ferrooxidans, IS256 from Staphylococcus aureus, and ISRm3 from Rhizobium meliloti. IS666 has 24 bp imperfect inverted repeats that fit the consensus described for the family, and generates 9 bp duplications upon insertion into the host DNA with no apparent specificity in the target sequence. In contrast with its two closest homologues, IS1166 and IS6120, IS666 contains a single ORF that would codify a transposase of 434 aa. IS666 is restricted to M. avium, where it is present in 21% of the isolates in a number ranging between 1 to 7 copies.","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/OMI.1.2000.5.181","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60513990","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Genome of human hepatitis C virus (HCV): gene organization, sequence diversity, and variation.","authors":"N. Kato","doi":"10.1089/OMI.1.2000.5.129","DOIUrl":"https://doi.org/10.1089/OMI.1.2000.5.129","url":null,"abstract":"Hepatitis C virus (HCV) is the major etiologic agent of non-A, non-B hepatitis. HCV infection frequently causes chronic hepatitis, which progresses to liver cirrhosis and hepatocellular carcinoma. Since the discovery of HCV in 1989, a large number of genetic analyses of HCV have been reported, and the viral genome structure has been elucidated. An enveloped virus, HCV belongs to the family Flaviviridae, whose genome consists of a positive-stranded RNA molecule of about 9.6 kilobases and encodes a large polyprotein precursor (about 3000 amino acids). This precursor protein is cleaved by the host and viral proteinase to generate at least 10 proteins: the core, envelope 1 (E1), E2, p7, nonstructural (NS) 2, NS3, NS4A, NS4B, NS5A, and NS5B. These HCV proteins not only function in viral replication but also affect a variety of cellular functions. HCV has been found to have remarkable genetic heterogeneity. To date, more than 30 HCV genotypes have been identified worldwide. Furthermore, HCV may show quasispecies distribution in an infected individual. These findings may have important implications in diagnosis, pathogenesis, treatment, and vaccine development. The hypervariable region 1 found within the envelope E2 protein was shown to be a major site for the genetic evolution of HCV after the onset of hepatitis, and might be involved in escape from the host immunesurveillance system.","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/OMI.1.2000.5.129","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60514276","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Relationship between whole proteome aminoacid composition and static DNA curvature.","authors":"R Jáuregui, F Bolivar, E Merino","doi":"10.1089/10906590050145221","DOIUrl":"https://doi.org/10.1089/10906590050145221","url":null,"abstract":"<p><p>To study possible relationships between an organism's genomic DNA curvature and the aminoacid composition of its proteome, every peptidic sequence from fully determined genomes was retrotranslated using the E. coli codon preferences, and the curvature profiles of the resulting DNA sequences were calculated and compared. A clear interdependence between these two variables was observed, as each retrotranslated proteome presented a distinctive, statistically significant DNA curvature profile biased toward its natural DNA curvature profile. In addition, by comparing the profiles arising from real and randomly permuted proteomes, we also found a position-dependent contribution of the peptidic sequence to DNA curvature. The implications of these results support the idea of a possible selection toward a specific global curvature of genomes.</p>","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/10906590050145221","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21844605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}