Literature DB >> 20008477

sORF finder: a program package to identify small open reading frames with high coding potential.

Kousuke Hanada1, Kenji Akiyama, Tetsuya Sakurai, Tetsuro Toyoda, Kazuo Shinozaki, Shin-Han Shiu.   

Abstract

SUMMARY: sORF finder is a program package for identifying small open reading frames (sORFs) with high-coding potential. This application allows the identification of coding sORFs according to the nucleotide composition bias among coding sequences and the potential functional constraint at the amino acid level through evaluation of synonymous and non-synonymous substitution rates. AVAILABILITY: Online tools and source codes are freely available at http://evolver.psc.riken.jp/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Mesh：

Year:  2009        PMID： 20008477     DOI： 10.1093/bioinformatics/btp688

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  38 in total

1.  Small open reading frames associated with morphogenesis are hidden in plant genomes.

Authors:  Kousuke Hanada; Mieko Higuchi-Takeuchi; Masanori Okamoto; Takeshi Yoshizumi; Minami Shimizu; Kentaro Nakaminami; Ranko Nishi; Chihiro Ohashi; Kei Iida; Maho Tanaka; Yoko Horii; Mika Kawashima; Keiko Matsui; Tetsuro Toyoda; Kazuo Shinozaki; Motoaki Seki; Minami Matsui
Journal:  Proc Natl Acad Sci U S A       Date:  2013-01-22       Impact factor: 11.205

Review 2.  Emerging evidence for functional peptides encoded by short open reading frames.

Authors:  Shea J Andrews; Joseph A Rothnagel
Journal:  Nat Rev Genet       Date:  2014-02-11       Impact factor: 53.242

3.  Drought stress differentially regulates the expression of small open reading frames (sORFs) in Arabidopsis roots and shoots.

Authors:  Sultana Rasheed; Khurram Bashir; Kentaro Nakaminami; Kousuke Hanada; Akihiro Matsui; Motoaki Seki
Journal:  Plant Signal Behav       Date:  2016-08-02

Review 4.  Identifying (non-)coding RNAs and small peptides: challenges and opportunities.

Authors:  Andrea Pauli; Eivind Valen; Alexander F Schier
Journal:  Bioessays       Date:  2014-10-24       Impact factor: 4.345

5.  AtPep3 is a hormone-like peptide that plays a role in the salinity stress tolerance of plants.

Authors:  Kentaro Nakaminami; Masanori Okamoto; Mieko Higuchi-Takeuchi; Takeshi Yoshizumi; Yube Yamaguchi; Yoichiro Fukao; Minami Shimizu; Chihiro Ohashi; Maho Tanaka; Minami Matsui; Kazuo Shinozaki; Motoaki Seki; Kousuke Hanada
Journal:  Proc Natl Acad Sci U S A       Date:  2018-05-14       Impact factor: 11.205

6.  MtSSPdb: The Medicago truncatula Small Secreted Peptide Database.

Authors:  Clarissa Boschiero; Xinbin Dai; Peter Knut Lundquist; Sonali Roy; Thomas Christian de Bang; Shulan Zhang; Zhaohong Zhuang; Ivone Torres-Jerez; Michael K Udvardi; Wolf-Rüdiger Scheible; Patrick Xuechun Zhao
Journal:  Plant Physiol       Date:  2020-02-20       Impact factor: 8.340

7.  Discovery and annotation of small proteins using genomics, proteomics, and computational approaches.

Authors:  Xiaohan Yang; Timothy J Tschaplinski; Gregory B Hurst; Sara Jawdy; Paul E Abraham; Patricia K Lankford; Rachel M Adams; Manesh B Shah; Robert L Hettich; Erika Lindquist; Udaya C Kalluri; Lee E Gunter; Christa Pennacchio; Gerald A Tuskan
Journal:  Genome Res       Date:  2011-03-02       Impact factor: 9.043

8.  Genome-Wide Identification of Medicago Peptides Involved in Macronutrient Responses and Nodulation.

Authors:  Thomas C de Bang; Peter K Lundquist; Xinbin Dai; Clarissa Boschiero; Zhaohong Zhuang; Pooja Pant; Ivone Torres-Jerez; Sonali Roy; Joaquina Nogales; Vijaykumar Veerappan; Rebecca Dickstein; Michael K Udvardi; Patrick X Zhao; Wolf-Rüdiger Scheible
Journal:  Plant Physiol       Date:  2017-10-13       Impact factor: 8.340

9.  Substantial expression of novel small open reading frames in Oryza sativa.

Authors:  Masanori Okamoto; Mieko Higuchi-Takeuchi; Minami Shimizu; Kazuo Shinozaki; Kousuke Hanada
Journal:  Plant Signal Behav       Date:  2014-02-13

10.  OCCAM: prediction of small ORFs in bacterial genomes by means of a target-decoy database approach and machine learning techniques.

Authors:  Fabio R Cerqueira; Ana Tereza Ribeiro Vasconcelos
Journal:  Database (Oxford)       Date:  2020-01-01       Impact factor: 3.451
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