Pub Date : 2001-11-01DOI: 10.1093/bioinformatics/17.11.997
N. Kolchanov, C. Hodgman
{"title":"The 2nd international conference on the Bioinformatics of Genome Regulation and Structure (BGRS-2000), Novosibirsk, August 2000","authors":"N. Kolchanov, C. Hodgman","doi":"10.1093/bioinformatics/17.11.997","DOIUrl":"https://doi.org/10.1093/bioinformatics/17.11.997","url":null,"abstract":"","PeriodicalId":90576,"journal":{"name":"Journal of bioinformatics","volume":"3 1","pages":"997"},"PeriodicalIF":0.0,"publicationDate":"2001-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88865441","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}
Pub Date : 2001-10-01DOI: 10.1093/bioinformatics/17.10.859
M. Borodovsky, E. Koonin, C. Burge, J. Fickett, J. Logsdon, A. Sali, G. Stormo, I. Zhulin
{"title":"The Third Georgia Tech-Emory International Conference on Bioinformatics: In Silico Biology; Bioinformatics After Human Genome (November 15-18, 2001, Atlanta, Georgia, USA)","authors":"M. Borodovsky, E. Koonin, C. Burge, J. Fickett, J. Logsdon, A. Sali, G. Stormo, I. Zhulin","doi":"10.1093/bioinformatics/17.10.859","DOIUrl":"https://doi.org/10.1093/bioinformatics/17.10.859","url":null,"abstract":"","PeriodicalId":90576,"journal":{"name":"Journal of bioinformatics","volume":"48 1","pages":"859-861"},"PeriodicalIF":0.0,"publicationDate":"2001-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77210215","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}
Pub Date : 2001-10-01DOI: 10.1093/BIOINFORMATICS/17.10.965
I. Jordan, G. Bishop, D. S. Gonzalez
Motivation: Class I α-mannosidases comprise a homologous and functionally diverse family of glycoside hydrolases. Phylogenetic analysis based on an amino acid sequence alignment of the catalytic domain of class I α-mannosidases reveals four well-supported phylogenetic groups within this family. These groups include a number of paralogous members generated by gene duplications that occurred as far back as the initial divergence of the crown-group of eukaryotes. Three of the four phylogenetic groups consist of enzymes that have group-specific biochemical specificity and/or sites of activity. An attempt has been made to uncover the role that natural selection played in the sequence and structural divergence between the phylogenetically and functionally distinct Endoplasmic Reticulum (ER) and Golgi apparatus groups. Results: Comparison of site-specific amino acid variability profiles for the ER and Golgi groups revealed statistically significant evidence for functional diversification at the sequence level and indicated a number of residues that are most likely to have played a role in the functional divergence between the two groups. The majority of these sites appear to contain residues that have been fixed within one organelle-specific group by positive selection. Somewhat surprisingly these selected residues map to the periphery of the α-mannosidase catalytic domain tertiary structure. Changes in these peripherally located residues would not seem to have a gross effect on protein function. Thus diversifying selection between the two groups may have acted in a gradual manner consistent with the Darwinian model of natural selection.
{"title":"Sequence and structural aspects of functional diversification in class I-mannosidase evolution","authors":"I. Jordan, G. Bishop, D. S. Gonzalez","doi":"10.1093/BIOINFORMATICS/17.10.965","DOIUrl":"https://doi.org/10.1093/BIOINFORMATICS/17.10.965","url":null,"abstract":"Motivation: Class I α-mannosidases comprise a homologous and functionally diverse family of glycoside hydrolases. Phylogenetic analysis based on an amino acid sequence alignment of the catalytic domain of class I α-mannosidases reveals four well-supported phylogenetic groups within this family. These groups include a number of paralogous members generated by gene duplications that occurred as far back as the initial divergence of the crown-group of eukaryotes. Three of the four phylogenetic groups consist of enzymes that have group-specific biochemical specificity and/or sites of activity. An attempt has been made to uncover the role that natural selection played in the sequence and structural divergence between the phylogenetically and functionally distinct Endoplasmic Reticulum (ER) and Golgi apparatus groups. Results: Comparison of site-specific amino acid variability profiles for the ER and Golgi groups revealed statistically significant evidence for functional diversification at the sequence level and indicated a number of residues that are most likely to have played a role in the functional divergence between the two groups. The majority of these sites appear to contain residues that have been fixed within one organelle-specific group by positive selection. Somewhat surprisingly these selected residues map to the periphery of the α-mannosidase catalytic domain tertiary structure. Changes in these peripherally located residues would not seem to have a gross effect on protein function. Thus diversifying selection between the two groups may have acted in a gradual manner consistent with the Darwinian model of natural selection.","PeriodicalId":90576,"journal":{"name":"Journal of bioinformatics","volume":"17 1","pages":"965-976"},"PeriodicalIF":0.0,"publicationDate":"2001-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90881069","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}
Pub Date : 2001-06-01DOI: 10.1093/BIOINFORMATICS/17.6.533
R. Apweiler, P. Kersey, Vivien L. Junker, A. Bairoch
In their paper “Database verification studies of SWISS-PROT and GenBank” Karp et al. (2001) conclude:(1) “SWISS-PROT is more incomplete than we ex-pected...”; (2) “Even if wecombine SWISS-PROTand TrEMBL, some sequences from the full genomesare missing from the combined dataset”; (3) “In manycases, translated GenBank genes do not exactly matchthe corresponding SWISS-PROT sequences, ...”; and(4) “...that SWISS-PROT does not identify a significantnumber of experimentally characterized proteins”.These results, and the approach used to arrive at theseresults, are in our opinion somewhat misleading. Herein,we only focus on four major points.First, there has never been a claim that SWISS-PROTis comprehensive. Thus, it is surprising that Karp et al.found that “SWISS-PROT is more incomplete than weexpected...”. To makesequences available as quickly aspossible without diluting the quality of SWISS-PROT,the supplemental database TrEMBL was introducedin 1996 and contains the translation of all coding se-quences (CDS) in the DDBJ/EMBL/GenBank nucleotidesequence database, except those already included inSWISS-PROT. Snapshots of the SWISS-PROT, TrEMBLand TrEMBLnew databases are released weekly, syn-chronised with the DDBJ/EMBL/GenBank nucleotidesequence database and provide comprehensive cover-age (ftp://ftp.ebi.ac.uk/pub/databases/sp tr nrdb/). Theweekly comprehensive SWISS-PROT/TrEMBL nonre-dundant database (SPTR) has been widely publicisedon the EBI and ExPASy web-servers and in variouspublications (e.g. Apweiler, 2000).Second, the authors’ assertions that “Even if wecombine SWISS-PROT and TrEMBL, some sequencesfrom the full genomes are missing from the com-bined dataset.” and “SWISS-PROT curators apparentlychose not to replace existing SWISS-PROT sequenceswith sequences from complete-genome projects” arerather inaccurate. Karp et al. tried to establish corre-sponding sets of SWISS-PROT/TrEMBL proteins and
Karp et al.(2001)在他们的论文“SWISS-PROT和GenBank的数据库验证研究”中得出结论:(1)“SWISS-PROT比我们预期的更不完整……”;(2)“即使我们将SWISS-PROTand TrEMBL组合在一起，一些全基因组序列也会在组合数据集中缺失”;(3)“在许多情况下，翻译的GenBank基因并不完全匹配相应的SWISS-PROT序列，…”;和(4)”……SWISS-PROT没有识别出大量实验表征的蛋白质”。在我们看来，这些结果，以及用来得出这些结果的方法，在某种程度上具有误导性。在此，我们只关注四点。首先，从来没有人声称SWISS-PROTis是全面的。因此，令人惊讶的是，Karp等人发现“SWISS-PROT比我们预期的更不完整……”。为了在不影响SWISS-PROT质量的情况下尽可能快地获得序列，1996年引入了补充数据库TrEMBL，该数据库包含DDBJ/EMBL/GenBank核苷酸序列数据库中除SWISS-PROT中已包含的外的所有编码序列(CDS)的翻译。瑞士- prot、TrEMBLand和TrEMBLnew数据库的快照每周发布一次，与DDBJ/EMBL/GenBank核苷酸序列数据库同步，并提供全面的覆盖范围(ftp://ftp.ebi.ac。Uk /pub/databases/sp tr nrdb/)。每周全面的SWISS-PROT/TrEMBL非冗余数据库(SPTR)已在EBI和ExPASy网络服务器和各种出版物上广泛宣传(例如Apweiler, 2000)。其次，作者断言，“即使我们将SWISS-PROT和TrEMBL结合起来，也会在合并后的数据集中缺少全基因组的一些序列。和“SWISS-PROT策展人显然没有选择用全基因组计划的序列取代现有的SWISS-PROT序列”是相当不准确的。Karp等人试图建立相应的SWISS-PROT/TrEMBL蛋白组和
{"title":"Technical comment to \"Database verification studies of SWISS-PROT and GenBank\" by Karp et al","authors":"R. Apweiler, P. Kersey, Vivien L. Junker, A. Bairoch","doi":"10.1093/BIOINFORMATICS/17.6.533","DOIUrl":"https://doi.org/10.1093/BIOINFORMATICS/17.6.533","url":null,"abstract":"In their paper “Database verification studies of SWISS-PROT and GenBank” Karp et al. (2001) conclude:(1) “SWISS-PROT is more incomplete than we ex-pected...”; (2) “Even if wecombine SWISS-PROTand TrEMBL, some sequences from the full genomesare missing from the combined dataset”; (3) “In manycases, translated GenBank genes do not exactly matchthe corresponding SWISS-PROT sequences, ...”; and(4) “...that SWISS-PROT does not identify a significantnumber of experimentally characterized proteins”.These results, and the approach used to arrive at theseresults, are in our opinion somewhat misleading. Herein,we only focus on four major points.First, there has never been a claim that SWISS-PROTis comprehensive. Thus, it is surprising that Karp et al.found that “SWISS-PROT is more incomplete than weexpected...”. To makesequences available as quickly aspossible without diluting the quality of SWISS-PROT,the supplemental database TrEMBL was introducedin 1996 and contains the translation of all coding se-quences (CDS) in the DDBJ/EMBL/GenBank nucleotidesequence database, except those already included inSWISS-PROT. Snapshots of the SWISS-PROT, TrEMBLand TrEMBLnew databases are released weekly, syn-chronised with the DDBJ/EMBL/GenBank nucleotidesequence database and provide comprehensive cover-age (ftp://ftp.ebi.ac.uk/pub/databases/sp tr nrdb/). Theweekly comprehensive SWISS-PROT/TrEMBL nonre-dundant database (SPTR) has been widely publicisedon the EBI and ExPASy web-servers and in variouspublications (e.g. Apweiler, 2000).Second, the authors’ assertions that “Even if wecombine SWISS-PROT and TrEMBL, some sequencesfrom the full genomes are missing from the com-bined dataset.” and “SWISS-PROT curators apparentlychose not to replace existing SWISS-PROT sequenceswith sequences from complete-genome projects” arerather inaccurate. Karp et al. tried to establish corre-sponding sets of SWISS-PROT/TrEMBL proteins and","PeriodicalId":90576,"journal":{"name":"Journal of bioinformatics","volume":"10 1","pages":"533-534"},"PeriodicalIF":0.0,"publicationDate":"2001-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84910427","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}
Pub Date : 2001-01-01DOI: 10.1093/bioinformatics/17.1.107
C. Helma, R. King, Stefan Kramer, A. Srinivasan
We initiated the Predictive Toxicology Challenge (PTC) to stimulate the development of advanced SAR techniques for predictive toxicology models. The goal of this challenge is to predict the rodent carcinogenicity of new compounds based on the experimental results of the US National Toxicology Program (NTP). Submissions will be evaluated on quantitative and qualitative scales to select the most predictive models and those with the highest toxicological relevance. Availability: http://www.informatik.uni-freiburg.de/∼ml/ptc/ Contact: helma@informatik.uni-freiburg.de.
{"title":"The Predictive Toxicology Challenge 2000-2001","authors":"C. Helma, R. King, Stefan Kramer, A. Srinivasan","doi":"10.1093/bioinformatics/17.1.107","DOIUrl":"https://doi.org/10.1093/bioinformatics/17.1.107","url":null,"abstract":"We initiated the Predictive Toxicology Challenge (PTC) to stimulate the development of advanced SAR techniques for predictive toxicology models. The goal of this challenge is to predict the rodent carcinogenicity of new compounds based on the experimental results of the US National Toxicology Program (NTP). Submissions will be evaluated on quantitative and qualitative scales to select the most predictive models and those with the highest toxicological relevance. Availability: http://www.informatik.uni-freiburg.de/∼ml/ptc/ Contact: helma@informatik.uni-freiburg.de.","PeriodicalId":90576,"journal":{"name":"Journal of bioinformatics","volume":"25 1","pages":"107-108"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87021537","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}
Pub Date : 2001-01-01DOI: 10.1093/bioinformatics/17.1.1
C. Sander
{"title":"Bioinformatics - Challenges in 2001","authors":"C. Sander","doi":"10.1093/bioinformatics/17.1.1","DOIUrl":"https://doi.org/10.1093/bioinformatics/17.1.1","url":null,"abstract":"","PeriodicalId":90576,"journal":{"name":"Journal of bioinformatics","volume":"29 1","pages":"1-2"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80854601","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}
Pub Date : 2000-11-01DOI: 10.1093/bioinformatics/16.11.1050
E. Beitz
UNLABELLED T(E)Xtopo is a LAT(E)X2epsilon macro package for plotting topology data directly from PHD predictions or SwissProt database files in publication-ready quality. The plot can be shaded automatically to emphasize conserved residues or functional properties of the residue sidechains. The addition of rich decorations, such as labels, annotations and legends, is easily accomplished. AVAILABILITY The T(E)Xtopo macro package and a full on-line documentation are freely available at http://homepages.uni-tuebingen.de/beitz/ CONTACT eric.beitz@uni-tuebingen.de
{"title":"TEXtopo: shaded membrane protein topology plots in LATEX2","authors":"E. Beitz","doi":"10.1093/bioinformatics/16.11.1050","DOIUrl":"https://doi.org/10.1093/bioinformatics/16.11.1050","url":null,"abstract":"UNLABELLED T(E)Xtopo is a LAT(E)X2epsilon macro package for plotting topology data directly from PHD predictions or SwissProt database files in publication-ready quality. The plot can be shaded automatically to emphasize conserved residues or functional properties of the residue sidechains. The addition of rich decorations, such as labels, annotations and legends, is easily accomplished. AVAILABILITY The T(E)Xtopo macro package and a full on-line documentation are freely available at http://homepages.uni-tuebingen.de/beitz/ CONTACT eric.beitz@uni-tuebingen.de","PeriodicalId":90576,"journal":{"name":"Journal of bioinformatics","volume":"29 1","pages":"1050-1051"},"PeriodicalIF":0.0,"publicationDate":"2000-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75091508","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}
Pub Date : 1999-12-01DOI: 10.1093/bioinformatics/15.12.955
David T Jones
{"title":"Bioinformatics and the Y2K Problem","authors":"David T Jones","doi":"10.1093/bioinformatics/15.12.955","DOIUrl":"https://doi.org/10.1093/bioinformatics/15.12.955","url":null,"abstract":"","PeriodicalId":90576,"journal":{"name":"Journal of bioinformatics","volume":"44 1","pages":"955-956"},"PeriodicalIF":0.0,"publicationDate":"1999-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79952250","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}
Pub Date : 1999-10-01DOI: 10.1093/bioinformatics/15.10.864
D. Fischer, D. Eisenberg
{"title":"Erratum. Finding families for genomic ORFans","authors":"D. Fischer, D. Eisenberg","doi":"10.1093/bioinformatics/15.10.864","DOIUrl":"https://doi.org/10.1093/bioinformatics/15.10.864","url":null,"abstract":"","PeriodicalId":90576,"journal":{"name":"Journal of bioinformatics","volume":"29 1","pages":"864"},"PeriodicalIF":0.0,"publicationDate":"1999-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85394300","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}
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