Literature DB >> 11864365

The past, present and future of genome-wide re-annotation.

Christos A Ouzounis1, Peter D Karp.   

Abstract

Annotation, the process by which structural or functional information is inferred for genes or proteins, is crucial for obtaining value from genome sequences. We define the process of annotating a previously annotated genome sequence as 're-annotation', and examine the strengths and weaknesses of current manual and automatic genome-wide re-annotation approaches.

Entities:  

Mesh：

Year:  2002        PMID： 11864365      PMCID： PMC139008          DOI： 10.1186/gb-2002-3-2-comment2001

Source DB:  PubMed          Journal:  Genome Biol        ISSN： 1474-7596            Impact factor:   13.583


  37 in total

1.  More Haemophilus and Mycoplasma genes.

Authors:  K Robison; W Gilbert; G M Church
Journal:  Science       Date:  1996-03-01       Impact factor: 47.728

2.  Predicting enzyme function from sequence: a systematic appraisal.

Authors:  I Shah; L Hunter
Journal:  Proc Int Conf Intell Syst Mol Biol       Date:  1997

3.  Prediction of enzyme classification from protein sequence without the use of sequence similarity.

Authors:  M des Jardins; P D Karp; M Krummenacker; T J Lee; C A Ouzounis
Journal:  Proc Int Conf Intell Syst Mol Biol       Date:  1997

4.  The challenges of genome sequence annotation or "the devil is in the details".

Authors:  T F Smith; X Zhang
Journal:  Nat Biotechnol       Date:  1997-11       Impact factor: 54.908

5.  HinCyc: a knowledge base of the complete genome and metabolic pathways of H. influenzae.

Authors:  P D Karp; C Ouzounis; S Paley
Journal:  Proc Int Conf Intell Syst Mol Biol       Date:  1996

6.  Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function.

Authors:  M Andrade; G Casari; A de Daruvar; C Sander; R Schneider; J Tamames; A Valencia; C Ouzounis
Journal:  Comput Appl Biosci       Date:  1997-08

7.  Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea.

Authors:  E V Koonin; A R Mushegian; M Y Galperin; D R Walker
Journal:  Mol Microbiol       Date:  1997-08       Impact factor: 3.501

8.  New protein functions in yeast chromosome VIII.

Authors:  C Ouzounis; P Bork; G Casari; C Sander
Journal:  Protein Sci       Date:  1995-11       Impact factor: 6.725

9.  Characterization of new proteins found by analysis of short open reading frames from the full yeast genome.

Authors:  M A Andrade; A Daruvar; G Casari; R Schneider; M Termier; C Sander
Journal:  Yeast       Date:  1997-11       Impact factor: 3.239

10.  Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli.

Authors:  R L Tatusov; A R Mushegian; P Bork; N P Brown; W S Hayes; M Borodovsky; K E Rudd; E V Koonin
Journal:  Curr Biol       Date:  1996-03-01       Impact factor: 10.834
View more
  52 in total

1.  DNannotator: Annotation software tool kit for regional genomic sequences.

Authors:  Chunyu Liu; Tom I Bonner; Tu Nguyen; Jennifer L Lyons; Susan L Christian; Elliot S Gershon
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

Review 2.  'Conserved hypothetical' proteins: prioritization of targets for experimental study.

Authors:  Michael Y Galperin; Eugene V Koonin
Journal:  Nucleic Acids Res       Date:  2004-10-12       Impact factor: 16.971

3.  Pathway analysis software: annotation errors and solutions.

Authors:  Nicole K Henderson-Maclennan; Jeanette C Papp; C Conover Talbot; Edward R B McCabe; Angela P Presson
Journal:  Mol Genet Metab       Date:  2010-06-22       Impact factor: 4.797

4.  EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference.

Authors:  Weidong Tian; Adrian K Arakaki; Jeffrey Skolnick
Journal:  Nucleic Acids Res       Date:  2004-12-01       Impact factor: 16.971

5.  Genome coverage, literally speaking. The challenge of annotating 200 genomes with 4 million publications.

Authors:  Paul Janssen; Leon Goldovsky; Victor Kunin; Nikos Darzentas; Christos A Ouzounis
Journal:  EMBO Rep       Date:  2005-05       Impact factor: 8.807

6.  Prediction of protein function improving sequence remote alignment search by a fuzzy logic algorithm.

Authors:  Antonio Gómez; Juan Cedano; Jordi Espadaler; Antonio Hermoso; Jaume Piñol; Enrique Querol
Journal:  Protein J       Date:  2008-02       Impact factor: 2.371

Review 7.  FINDSITE: a combined evolution/structure-based approach to protein function prediction.

Authors:  Jeffrey Skolnick; Michal Brylinski
Journal:  Brief Bioinform       Date:  2009-03-26       Impact factor: 11.622

8.  SHARP: genome-scale identification of gene-protein-reaction associations in cyanobacteria.

Authors:  S Krishnakumar; Dilip A Durai; Pramod P Wangikar; Ganesh A Viswanathan
Journal:  Photosynth Res       Date:  2013-08-24       Impact factor: 3.573

9.  Evaluation of probabilistic and logical inference for a SNP annotation system.

Authors:  Terry H Shen; Peter Tarczy-Hornoch; Landon T Detwiler; Eithon Cadag; Christopher S Carlson
Journal:  J Biomed Inform       Date:  2009-12-14       Impact factor: 6.317

10.  GenoQuery: a new querying module for functional annotation in a genomic warehouse.

Authors:  Frédéric Lemoine; Bernard Labedan; Christine Froidevaux
Journal:  Bioinformatics       Date:  2008-07-01       Impact factor: 6.937
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.