Literature DB >> 18629076

Unravelling the ORFan Puzzle.

Naomi Siew1, Daniel Fischer.   

Abstract

ORFans are open reading frames (ORFs) with no detectable sequence similarity to any other sequence in the databases. Each newly sequenced genome contains a significant number of ORFans. Therefore, ORFans entail interesting evolutionary puzzles. However, little can be learned about them using bioinformatics tools, and their study seems to have been underemphasized. Here we present some of the questions that the existence of so many ORFans have raised and review some of the studies aimed at understanding ORFans, their functions and their origins. These works have demonstrated that ORFans are an untapped source of research, requiring further computational and experimental studies.

Year:  2003        PMID: 18629076      PMCID: PMC2447361          DOI: 10.1002/cfg.311

Source DB:  PubMed          Journal:  Comp Funct Genomics        ISSN: 1531-6912


  50 in total

1.  Finding families for genomic ORFans.

Authors:  D Fischer; D Eisenberg
Journal:  Bioinformatics       Date:  1999-09       Impact factor: 6.937

2.  Emergence of scaling in random networks

Authors: 
Journal:  Science       Date:  1999-10-15       Impact factor: 47.728

3.  Protein dispensability and rate of evolution.

Authors:  A E Hirsh; H B Fraser
Journal:  Nature       Date:  2001-06-28       Impact factor: 49.962

Review 4.  Microbial genomes: dealing with diversity.

Authors:  Y Boucher; C L Nesbø; W F Doolittle
Journal:  Curr Opin Microbiol       Date:  2001-06       Impact factor: 7.934

5.  Global transposon mutagenesis and a minimal Mycoplasma genome.

Authors:  C A Hutchison; S N Peterson; S R Gill; R T Cline; O White; C M Fraser; H O Smith; J C Venter
Journal:  Science       Date:  1999-12-10       Impact factor: 47.728

6.  The frequency distribution of gene family sizes in complete genomes.

Authors:  M A Huynen; E van Nimwegen
Journal:  Mol Biol Evol       Date:  1998-05       Impact factor: 16.240

7.  Origin and properties of non-coding ORFs in the yeast genome.

Authors:  P Mackiewicz; M Kowalczuk; A Gierlik; M R Dudek; S Cebrat
Journal:  Nucleic Acids Res       Date:  1999-09-01       Impact factor: 16.971

8.  The evolutionary analysis of "orphans" from the Drosophila genome identifies rapidly diverging and incorrectly annotated genes.

Authors:  K J Schmid; C F Aquadro
Journal:  Genetics       Date:  2001-10       Impact factor: 4.562

9.  Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori.

Authors:  R A Alm; L S Ling; D T Moir; B L King; E D Brown; P C Doig; D R Smith; B Noonan; B C Guild; B L deJonge; G Carmel; P J Tummino; A Caruso; M Uria-Nickelsen; D M Mills; C Ives; R Gibson; D Merberg; S D Mills; Q Jiang; D E Taylor; G F Vovis; T J Trust
Journal:  Nature       Date:  1999-01-14       Impact factor: 49.962

10.  Myriads of protein families, and still counting.

Authors:  Victor Kunin; Ildefonso Cases; Anton J Enright; Victor de Lorenzo; Christos A Ouzounis
Journal:  Genome Biol       Date:  2003-01-28       Impact factor: 13.583

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  12 in total

1.  The ORFanage: an ORFan database.

Authors:  Naomi Siew; Yaniv Azaria; Daniel Fischer
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

2.  Dynamic behavior of an intrinsically unstructured linker domain is conserved in the face of negligible amino acid sequence conservation.

Authors:  Gary W Daughdrill; Pranesh Narayanaswami; Sara H Gilmore; Agniezka Belczyk; Celeste J Brown
Journal:  J Mol Evol       Date:  2007-08-25       Impact factor: 2.395

3.  Hypothetical proteins present during recovery phase of radiation resistant bacterium Deinococcus radiodurans are under purifying selection.

Authors:  Anubrata D Das; Hari S Misra
Journal:  J Mol Evol       Date:  2013-08-10       Impact factor: 2.395

4.  Yaravirus: A novel 80-nm virus infecting Acanthamoeba castellanii.

Authors:  Paulo V M Boratto; Graziele P Oliveira; Talita B Machado; Ana Cláudia S P Andrade; Jean-Pierre Baudoin; Thomas Klose; Frederik Schulz; Saïd Azza; Philippe Decloquement; Eric Chabrière; Philippe Colson; Anthony Levasseur; Bernard La Scola; Jônatas S Abrahão
Journal:  Proc Natl Acad Sci U S A       Date:  2020-06-29       Impact factor: 11.205

5.  Disentangling the effects of selection and loss bias on gene dynamics.

Authors:  Jaime Iranzo; José A Cuesta; Susanna Manrubia; Mikhail I Katsnelson; Eugene V Koonin
Journal:  Proc Natl Acad Sci U S A       Date:  2017-06-26       Impact factor: 11.205

6.  Novel genes exhibit distinct patterns of function acquisition and network integration.

Authors:  John A Capra; Katherine S Pollard; Mona Singh
Journal:  Genome Biol       Date:  2010-12-27       Impact factor: 13.583

7.  On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer.

Authors:  Yanbin Yin; Daniel Fischer
Journal:  BMC Evol Biol       Date:  2006-08-16       Impact factor: 3.260

8.  Re-annotation of protein-coding genes in the genome of saccharomyces cerevisiae based on support vector machines.

Authors:  Dan Lin; Xin Yin; Xianlong Wang; Peng Zhou; Feng-Biao Guo
Journal:  PLoS One       Date:  2013-07-10       Impact factor: 3.240

9.  Identification and investigation of ORFans in the viral world.

Authors:  Yanbin Yin; Daniel Fischer
Journal:  BMC Genomics       Date:  2008-01-19       Impact factor: 3.969

10.  Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering.

Authors:  Shibu Yooseph; Weizhong Li; Granger Sutton
Journal:  BMC Bioinformatics       Date:  2008-04-10       Impact factor: 3.169

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