Literature DB >> 10745997

Shufflet: shuffling sequences while conserving the k-let counts.

E Coward1.   

Abstract

Shufflet is a program and a web-application that generates fast random shufflings of sequences (DNA, protein or others), conserving the exact k-let counts for a given k. The sequences are sampled uniformly from all the valid permutations.

Mesh：

Year:  1999        PMID： 10745997     DOI： 10.1093/bioinformatics/15.12.1058

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


  12 in total

Review 1.  Computational approaches to identify promoters and cis-regulatory elements in plant genomes.

Authors:  Stephane Rombauts; Kobe Florquin; Magali Lescot; Kathleen Marchal; Pierre Rouzé; Yves van de Peer
Journal:  Plant Physiol       Date:  2003-07       Impact factor: 8.340

2.  Unique folding of precursor microRNAs: quantitative evidence and implications for de novo identification.

Authors:  Stanley Ng Kwang Loong; Santosh K Mishra
Journal:  RNA       Date:  2006-12-28       Impact factor: 4.942

3.  On the estimation of false positives in peptide identifications using decoy search strategy.

Authors:  Changyu Shen; Quanhu Sheng; Jie Dai; Yixue Li; Rong Zeng; Haixu Tang
Journal:  Proteomics       Date:  2009-01       Impact factor: 3.984

4.  Natural selection retains overrepresented out-of-frame stop codons against frameshift peptides in prokaryotes.

Authors:  Herman Tse; James J Cai; Hoi-Wah Tsoi; Esther Pt Lam; Kwok-Yung Yuen
Journal:  BMC Genomics       Date:  2010-09-09       Impact factor: 3.969

5.  Stem-loop structures in prokaryotic genomes.

Authors:  Mauro Petrillo; Giustina Silvestro; Pier Paolo Di Nocera; Angelo Boccia; Giovanni Paolella
Journal:  BMC Genomics       Date:  2006-07-04       Impact factor: 3.969

6.  rMotifGen: random motif generator for DNA and protein sequences.

Authors:  Eric C Rouchka; C Timothy Hardin
Journal:  BMC Bioinformatics       Date:  2007-08-07       Impact factor: 3.169

7.  Current awareness on comparative and functional genomics.

Authors: 
Journal:  Yeast       Date:  2000-09-30       Impact factor: 3.239

8.  uShuffle: a useful tool for shuffling biological sequences while preserving the k-let counts.

Authors:  Minghui Jiang; James Anderson; Joel Gillespie; Martin Mayne
Journal:  BMC Bioinformatics       Date:  2008-04-11       Impact factor: 3.169

9.  Ancient duplicated conserved noncoding elements in vertebrates: a genomic and functional analysis.

Authors:  Gayle K McEwen; Adam Woolfe; Debbie Goode; Tanya Vavouri; Heather Callaway; Greg Elgar
Journal:  Genome Res       Date:  2006-03-13       Impact factor: 9.043

10.  Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences.

Authors:  Yanzhi Guo; Lezheng Yu; Zhining Wen; Menglong Li
Journal:  Nucleic Acids Res       Date:  2008-04-04       Impact factor: 16.971
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