Trawler Web

An online de novo motif discovery tool for next-generation sequencing datasets

Louis T. Dang, Markus Tondl, Man Ho H. Chiu, Jerico Revote, Benedict Paten, Vincent Tano, Alex Tokolyi, Florence Besse, Greg Quaife-Ryan, Helen Cumming, Mark J. Drvodelic, Michael P. Eichenlaub, Jeannette C. Hallab, Julian S. Stolper, Fernando J. Rossello, Marie A. Bogoyevitch, David A. Jans, Hieu T. Nim, Enzo R. Porrello, James E. Hudson & 1 others Mirana Ramialison

Research output: Contribution to journalArticleResearchpeer-review

2 Citations (Scopus)

Abstract

Background: A strong focus of the post-genomic era is mining of the non-coding regulatory genome in order to unravel the function of regulatory elements that coordinate gene expression (Nat 489:57-74, 2012; Nat 507:462-70, 2014; Nat 507:455-61, 2014; Nat 518:317-30, 2015). Whole-genome approaches based on next-generation sequencing (NGS) have provided insight into the genomic location of regulatory elements throughout different cell types, organs and organisms. These technologies are now widespread and commonly used in laboratories from various fields of research. This highlights the need for fast and user-friendly software tools dedicated to extracting cis-regulatory information contained in these regulatory regions; for instance transcription factor binding site (TFBS) composition. Ideally, such tools should not require prior programming knowledge to ensure they are accessible for all users. Results: We present TrawlerWeb, a web-based version of the Trawler_standalone tool (Nat Methods 4:563-5, 2007; Nat Protoc 5:323-34, 2010), to allow for the identification of enriched motifs in DNA sequences obtained from next-generation sequencing experiments in order to predict their TFBS composition. TrawlerWeb is designed for online queries with standard options common to web-based motif discovery tools. In addition, TrawlerWeb provides three unique new features: 1) TrawlerWeb allows the input of BED files directly generated from NGS experiments, 2) it automatically generates an input-matched biologically relevant background, and 3) it displays resulting conservation scores for each instance of the motif found in the input sequences, which assists the researcher in prioritising the motifs to validate experimentally. Finally, to date, this web-based version of Trawler_standalone remains the fastest online de novo motif discovery tool compared to other popular web-based software, while generating predictions with high accuracy. Conclusions: TrawlerWeb provides users with a fast, simple and easy-to-use web interface for de novo motif discovery. This will assist in rapidly analysing NGS datasets that are now being routinely generated. TrawlerWeb is freely available and accessible at: http://trawler.erc.monash.edu.au.

Original languageEnglish
Article number238
Number of pages9
JournalBMC Genomics
Volume19
Issue number1
DOIs
Publication statusPublished - 5 Apr 2018

Keywords

  • Chromatin immunoprecipitation
  • Motif conservation
  • Motif discovery
  • Next generation sequencing
  • Transcription factor binding site

Cite this

Dang, Louis T. ; Tondl, Markus ; Chiu, Man Ho H. ; Revote, Jerico ; Paten, Benedict ; Tano, Vincent ; Tokolyi, Alex ; Besse, Florence ; Quaife-Ryan, Greg ; Cumming, Helen ; Drvodelic, Mark J. ; Eichenlaub, Michael P. ; Hallab, Jeannette C. ; Stolper, Julian S. ; Rossello, Fernando J. ; Bogoyevitch, Marie A. ; Jans, David A. ; Nim, Hieu T. ; Porrello, Enzo R. ; Hudson, James E. ; Ramialison, Mirana. / Trawler Web : An online de novo motif discovery tool for next-generation sequencing datasets. In: BMC Genomics. 2018 ; Vol. 19, No. 1.
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abstract = "Background: A strong focus of the post-genomic era is mining of the non-coding regulatory genome in order to unravel the function of regulatory elements that coordinate gene expression (Nat 489:57-74, 2012; Nat 507:462-70, 2014; Nat 507:455-61, 2014; Nat 518:317-30, 2015). Whole-genome approaches based on next-generation sequencing (NGS) have provided insight into the genomic location of regulatory elements throughout different cell types, organs and organisms. These technologies are now widespread and commonly used in laboratories from various fields of research. This highlights the need for fast and user-friendly software tools dedicated to extracting cis-regulatory information contained in these regulatory regions; for instance transcription factor binding site (TFBS) composition. Ideally, such tools should not require prior programming knowledge to ensure they are accessible for all users. Results: We present TrawlerWeb, a web-based version of the Trawler_standalone tool (Nat Methods 4:563-5, 2007; Nat Protoc 5:323-34, 2010), to allow for the identification of enriched motifs in DNA sequences obtained from next-generation sequencing experiments in order to predict their TFBS composition. TrawlerWeb is designed for online queries with standard options common to web-based motif discovery tools. In addition, TrawlerWeb provides three unique new features: 1) TrawlerWeb allows the input of BED files directly generated from NGS experiments, 2) it automatically generates an input-matched biologically relevant background, and 3) it displays resulting conservation scores for each instance of the motif found in the input sequences, which assists the researcher in prioritising the motifs to validate experimentally. Finally, to date, this web-based version of Trawler_standalone remains the fastest online de novo motif discovery tool compared to other popular web-based software, while generating predictions with high accuracy. Conclusions: TrawlerWeb provides users with a fast, simple and easy-to-use web interface for de novo motif discovery. This will assist in rapidly analysing NGS datasets that are now being routinely generated. TrawlerWeb is freely available and accessible at: http://trawler.erc.monash.edu.au.",
keywords = "Chromatin immunoprecipitation, Motif conservation, Motif discovery, Next generation sequencing, Transcription factor binding site",
author = "Dang, {Louis T.} and Markus Tondl and Chiu, {Man Ho H.} and Jerico Revote and Benedict Paten and Vincent Tano and Alex Tokolyi and Florence Besse and Greg Quaife-Ryan and Helen Cumming and Drvodelic, {Mark J.} and Eichenlaub, {Michael P.} and Hallab, {Jeannette C.} and Stolper, {Julian S.} and Rossello, {Fernando J.} and Bogoyevitch, {Marie A.} and Jans, {David A.} and Nim, {Hieu T.} and Porrello, {Enzo R.} and Hudson, {James E.} and Mirana Ramialison",
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doi = "10.1186/s12864-018-4630-0",
language = "English",
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Dang, LT, Tondl, M, Chiu, MHH, Revote, J, Paten, B, Tano, V, Tokolyi, A, Besse, F, Quaife-Ryan, G, Cumming, H, Drvodelic, MJ, Eichenlaub, MP, Hallab, JC, Stolper, JS, Rossello, FJ, Bogoyevitch, MA, Jans, DA, Nim, HT, Porrello, ER, Hudson, JE & Ramialison, M 2018, 'Trawler Web: An online de novo motif discovery tool for next-generation sequencing datasets', BMC Genomics, vol. 19, no. 1, 238. https://doi.org/10.1186/s12864-018-4630-0

Trawler Web : An online de novo motif discovery tool for next-generation sequencing datasets. / Dang, Louis T.; Tondl, Markus; Chiu, Man Ho H.; Revote, Jerico; Paten, Benedict; Tano, Vincent; Tokolyi, Alex; Besse, Florence; Quaife-Ryan, Greg; Cumming, Helen; Drvodelic, Mark J.; Eichenlaub, Michael P.; Hallab, Jeannette C.; Stolper, Julian S.; Rossello, Fernando J.; Bogoyevitch, Marie A.; Jans, David A.; Nim, Hieu T.; Porrello, Enzo R.; Hudson, James E.; Ramialison, Mirana.

In: BMC Genomics, Vol. 19, No. 1, 238, 05.04.2018.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Trawler Web

T2 - An online de novo motif discovery tool for next-generation sequencing datasets

AU - Dang, Louis T.

AU - Tondl, Markus

AU - Chiu, Man Ho H.

AU - Revote, Jerico

AU - Paten, Benedict

AU - Tano, Vincent

AU - Tokolyi, Alex

AU - Besse, Florence

AU - Quaife-Ryan, Greg

AU - Cumming, Helen

AU - Drvodelic, Mark J.

AU - Eichenlaub, Michael P.

AU - Hallab, Jeannette C.

AU - Stolper, Julian S.

AU - Rossello, Fernando J.

AU - Bogoyevitch, Marie A.

AU - Jans, David A.

AU - Nim, Hieu T.

AU - Porrello, Enzo R.

AU - Hudson, James E.

AU - Ramialison, Mirana

PY - 2018/4/5

Y1 - 2018/4/5

N2 - Background: A strong focus of the post-genomic era is mining of the non-coding regulatory genome in order to unravel the function of regulatory elements that coordinate gene expression (Nat 489:57-74, 2012; Nat 507:462-70, 2014; Nat 507:455-61, 2014; Nat 518:317-30, 2015). Whole-genome approaches based on next-generation sequencing (NGS) have provided insight into the genomic location of regulatory elements throughout different cell types, organs and organisms. These technologies are now widespread and commonly used in laboratories from various fields of research. This highlights the need for fast and user-friendly software tools dedicated to extracting cis-regulatory information contained in these regulatory regions; for instance transcription factor binding site (TFBS) composition. Ideally, such tools should not require prior programming knowledge to ensure they are accessible for all users. Results: We present TrawlerWeb, a web-based version of the Trawler_standalone tool (Nat Methods 4:563-5, 2007; Nat Protoc 5:323-34, 2010), to allow for the identification of enriched motifs in DNA sequences obtained from next-generation sequencing experiments in order to predict their TFBS composition. TrawlerWeb is designed for online queries with standard options common to web-based motif discovery tools. In addition, TrawlerWeb provides three unique new features: 1) TrawlerWeb allows the input of BED files directly generated from NGS experiments, 2) it automatically generates an input-matched biologically relevant background, and 3) it displays resulting conservation scores for each instance of the motif found in the input sequences, which assists the researcher in prioritising the motifs to validate experimentally. Finally, to date, this web-based version of Trawler_standalone remains the fastest online de novo motif discovery tool compared to other popular web-based software, while generating predictions with high accuracy. Conclusions: TrawlerWeb provides users with a fast, simple and easy-to-use web interface for de novo motif discovery. This will assist in rapidly analysing NGS datasets that are now being routinely generated. TrawlerWeb is freely available and accessible at: http://trawler.erc.monash.edu.au.

AB - Background: A strong focus of the post-genomic era is mining of the non-coding regulatory genome in order to unravel the function of regulatory elements that coordinate gene expression (Nat 489:57-74, 2012; Nat 507:462-70, 2014; Nat 507:455-61, 2014; Nat 518:317-30, 2015). Whole-genome approaches based on next-generation sequencing (NGS) have provided insight into the genomic location of regulatory elements throughout different cell types, organs and organisms. These technologies are now widespread and commonly used in laboratories from various fields of research. This highlights the need for fast and user-friendly software tools dedicated to extracting cis-regulatory information contained in these regulatory regions; for instance transcription factor binding site (TFBS) composition. Ideally, such tools should not require prior programming knowledge to ensure they are accessible for all users. Results: We present TrawlerWeb, a web-based version of the Trawler_standalone tool (Nat Methods 4:563-5, 2007; Nat Protoc 5:323-34, 2010), to allow for the identification of enriched motifs in DNA sequences obtained from next-generation sequencing experiments in order to predict their TFBS composition. TrawlerWeb is designed for online queries with standard options common to web-based motif discovery tools. In addition, TrawlerWeb provides three unique new features: 1) TrawlerWeb allows the input of BED files directly generated from NGS experiments, 2) it automatically generates an input-matched biologically relevant background, and 3) it displays resulting conservation scores for each instance of the motif found in the input sequences, which assists the researcher in prioritising the motifs to validate experimentally. Finally, to date, this web-based version of Trawler_standalone remains the fastest online de novo motif discovery tool compared to other popular web-based software, while generating predictions with high accuracy. Conclusions: TrawlerWeb provides users with a fast, simple and easy-to-use web interface for de novo motif discovery. This will assist in rapidly analysing NGS datasets that are now being routinely generated. TrawlerWeb is freely available and accessible at: http://trawler.erc.monash.edu.au.

KW - Chromatin immunoprecipitation

KW - Motif conservation

KW - Motif discovery

KW - Next generation sequencing

KW - Transcription factor binding site

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