Literature DB >> 17151342

Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA.

Eva K Freyhult1, Jonathan P Bollback, Paul P Gardner.   

Abstract

Homology search is one of the most ubiquitous bioinformatic tasks, yet it is unknown how effective the currently available tools are for identifying noncoding RNAs (ncRNAs). In this work, we use reliable ncRNA data sets to assess the effectiveness of methods such as BLAST, FASTA, HMMer, and Infernal. Surprisingly, the most popular homology search methods are often the least accurate. As a result, many studies have used inappropriate tools for their analyses. On the basis of our results, we suggest homology search strategies using the currently available tools and some directions for future development.

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Year:  2006        PMID： 17151342      PMCID： PMC1716261          DOI： 10.1101/gr.5890907

Source DB:  PubMed          Journal:  Genome Res        ISSN： 1088-9051            Impact factor:   9.043


  50 in total

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Authors:  Maciej Szymanski; Miroslawa Z Barciszewska; Volker A Erdmann; Jan Barciszewski
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

2.  Empirical and hierarchical Bayesian estimation of ancestral states.

Authors:  J P Huelsenbeck; J P Bollback
Journal:  Syst Biol       Date:  2001-06       Impact factor: 15.683

3.  Secondary structure prediction for aligned RNA sequences.

Authors:  Ivo L Hofacker; Martin Fekete; Peter F Stadler
Journal:  J Mol Biol       Date:  2002-06-21       Impact factor: 5.469

4.  Mapping mutations on phylogenies.

Authors:  Rasmus Nielsen
Journal:  Syst Biol       Date:  2002-10       Impact factor: 15.683

5.  Rfam: an RNA family database.

Authors:  Sam Griffiths-Jones; Alex Bateman; Mhairi Marshall; Ajay Khanna; Sean R Eddy
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

6.  A comparison of profile hidden Markov model procedures for remote homology detection.

Authors:  Martin Madera; Julian Gough
Journal:  Nucleic Acids Res       Date:  2002-10-01       Impact factor: 16.971

7.  Detecting distant homologs using phylogenetic tree-based HMMs.

Authors:  Bin Qian; Richard A Goldstein
Journal:  Proteins       Date:  2003-08-15

8.  A hidden Markov model for progressive multiple alignment.

Authors:  Ari Löytynoja; Michel C Milinkovitch
Journal:  Bioinformatics       Date:  2003-08-12       Impact factor: 6.937

9.  Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms.

Authors:  W R Pearson
Journal:  Genomics       Date:  1991-11       Impact factor: 5.736

10.  Comparison of K+-channel genes within the genomes of Anopheles gambiae and Drosophila melanogaster.

Authors:  Thomas J McCormack
Journal:  Genome Biol       Date:  2003-08-20       Impact factor: 13.583
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  55 in total

1.  PSSMTS: position specific scoring matrices on tree structures.

Authors:  Kengo Sato; Kensuke Morita; Yasubumi Sakakibara
Journal:  J Math Biol       Date:  2007-07-07       Impact factor: 2.259

2.  Infernal 1.0: inference of RNA alignments.

Authors:  Eric P Nawrocki; Diana L Kolbe; Sean R Eddy
Journal:  Bioinformatics       Date:  2009-03-23       Impact factor: 6.937

3.  Comparative analysis of distinct non-coding characteristics potentially contributing to the divergence of human tissue-specific genes.

Authors:  Qianli Huang; Jiaming Guo; Qq Ge; Jesse Li-Ling; Xueping Chen; Fei Ma
Journal:  Genetica       Date:  2008-09-25       Impact factor: 1.082

4.  The tedious task of finding homologous noncoding RNA genes.

Authors:  Peter Menzel; Jan Gorodkin; Peter F Stadler
Journal:  RNA       Date:  2009-10-27       Impact factor: 4.942

5.  A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria.

Authors:  Joanna L McKenzie; Jennifer Robson; Michael Berney; Tony C Smith; Alaine Ruthe; Paul P Gardner; Vickery L Arcus; Gregory M Cook
Journal:  J Bacteriol       Date:  2012-02-24       Impact factor: 3.490

6.  Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families.

Authors:  Lars Barquist; Sarah W Burge; Paul P Gardner
Journal:  Curr Protoc Bioinformatics       Date:  2016-06-20

Review 7.  Computational analysis of noncoding RNAs.

Authors:  Stefan Washietl; Sebastian Will; David A Hendrix; Loyal A Goff; John L Rinn; Bonnie Berger; Manolis Kellis
Journal:  Wiley Interdiscip Rev RNA       Date:  2012-09-18       Impact factor: 9.957

8.  Group I introns are widespread in archaea.

Authors:  Eric P Nawrocki; Thomas A Jones; Sean R Eddy
Journal:  Nucleic Acids Res       Date:  2018-09-06       Impact factor: 16.971

9.  RScan: fast searching structural similarities for structured RNAs in large databases.

Authors:  Chenghai Xue; Guo-Ping Liu
Journal:  BMC Genomics       Date:  2007-07-31       Impact factor: 3.969

10.  A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi.

Authors:  Timothy T Perkins; Robert A Kingsley; Maria C Fookes; Paul P Gardner; Keith D James; Lu Yu; Samuel A Assefa; Miao He; Nicholas J Croucher; Derek J Pickard; Duncan J Maskell; Julian Parkhill; Jyoti Choudhary; Nicholas R Thomson; Gordon Dougan
Journal:  PLoS Genet       Date:  2009-07-17       Impact factor: 5.917
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