Journal of bioinformatics最新文献_第4页

Erratum: Evaluation of methods for the prediction of membrane spanning regions 勘误:评价预测膜跨越区域的方法

Journal of bioinformatics Pub Date : 2002-01-01 DOI: 10.1093/bioinformatics/18.1.218

Steffen Möller, M. Croning, R. Apweiler

引用次数: 14

The 2nd international conference on the Bioinformatics of Genome Regulation and Structure (BGRS-2000), Novosibirsk, August 2000 第二届基因组调控与结构生物信息学国际会议(BGRS-2000)，新西伯利亚，2000年8月

Journal of bioinformatics Pub Date : 2001-11-01 DOI: 10.1093/bioinformatics/17.11.997

N. Kolchanov, C. Hodgman

引用次数: 2

The Third Georgia Tech-Emory International Conference on Bioinformatics: In Silico Biology; Bioinformatics After Human Genome (November 15-18, 2001, Atlanta, Georgia, USA) 第三届佐治亚理工大学-埃默里大学生物信息学国际会议:硅生物学;人类基因组后的生物信息学(2001年11月15-18日，美国乔治亚州亚特兰大)

Journal of bioinformatics Pub Date : 2001-10-01 DOI: 10.1093/bioinformatics/17.10.859

M. Borodovsky, E. Koonin, C. Burge, J. Fickett, J. Logsdon, A. Sali, G. Stormo, I. Zhulin

引用次数: 0

Sequence and structural aspects of functional diversification in class I-mannosidase evolution i类甘露糖苷酶进化中功能多样化的序列和结构方面

Journal of bioinformatics Pub Date : 2001-10-01 DOI: 10.1093/BIOINFORMATICS/17.10.965

I. Jordan, G. Bishop, D. S. Gonzalez

{"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":null,"pages":null},"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}

引用次数: 14

Technical comment to "Database verification studies of SWISS-PROT and GenBank" by Karp et al 对Karp等人“SWISS-PROT和GenBank的数据库验证研究”的技术评论

Journal of bioinformatics Pub Date : 2001-06-01 DOI: 10.1093/BIOINFORMATICS/17.6.533

R. Apweiler, P. Kersey, Vivien L. Junker, A. Bairoch

{"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":null,"pages":null},"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}

引用次数: 8

Bioinformatics needs to adopt statistical thinking - Editorial 生物信息学需要采用统计思维

Journal of bioinformatics Pub Date : 2001-05-01 DOI: 10.1093/bioinformatics/17.5.389

M. Vingron

引用次数: 9

The Predictive Toxicology Challenge 2000-2001 预测毒理学挑战2000-2001

Journal of bioinformatics Pub Date : 2001-01-01 DOI: 10.1093/bioinformatics/17.1.107

C. Helma, R. King, Stefan Kramer, A. Srinivasan

引用次数: 221

Bioinformatics - Challenges in 2001 生物信息学- 2001年的挑战

Journal of bioinformatics Pub Date : 2001-01-01 DOI: 10.1093/bioinformatics/17.1.1

C. Sander

引用次数: 10

TEXtopo: shaded membrane protein topology plots in LATEX2 TEXtopo: LATEX2中阴影膜蛋白拓扑图

Journal of bioinformatics Pub Date : 2000-11-01 DOI: 10.1093/bioinformatics/16.11.1050

E. Beitz

引用次数: 65

Bioinformatics and the Y2K Problem 生物信息学与千年虫问题

Journal of bioinformatics Pub Date : 1999-12-01 DOI: 10.1093/bioinformatics/15.12.955

David T Jones

引用次数: 0