Literature DB >> 17660203

BLISS 2.0: a web-based tool for predicting conserved regulatory modules in distantly-related orthologous sequences.

Hailong Meng1, Arunava Banerjee, Lei Zhou.   

Abstract

UNLABELLED: BLISS 2.0 is a web-based application for identifying conserved regulatory modules in distantly related orthologous sequences. Unlike existing approaches, it performs the cross-genome comparison at the binding site level. Experimental results on simulated and real world data indicate that BLISS 2.0 can identify conserved regulatory modules from sequences with little overall similarity at the DNA sequence level. AVAILABILITY: http://www.blisstool.org/

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Year:  2007        PMID： 17660203      PMCID： PMC2584781          DOI： 10.1093/bioinformatics/btm368

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


  8 in total

1.  CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments.

Authors:  Roded Sharan; Ivan Ovcharenko; Asa Ben-Hur; Richard M Karp
Journal:  Bioinformatics       Date:  2003       Impact factor: 6.937

2.  ConSite: web-based prediction of regulatory elements using cross-species comparison.

Authors:  Albin Sandelin; Wyeth W Wasserman; Boris Lenhard
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

3.  rVISTA 2.0: evolutionary analysis of transcription factor binding sites.

Authors:  Gabriela G Loots; Ivan Ovcharenko
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

4.  TRANSFAC: transcriptional regulation, from patterns to profiles.

Authors:  V Matys; E Fricke; R Geffers; E Gössling; M Haubrock; R Hehl; K Hornischer; D Karas; A E Kel; O V Kel-Margoulis; D-U Kloos; S Land; B Lewicki-Potapov; H Michael; R Münch; I Reuter; S Rotert; H Saxel; M Scheer; S Thiele; E Wingender
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

5.  TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis.

Authors:  Stein Aerts; Peter Van Loo; Gert Thijs; Herbert Mayer; Rainer de Martin; Yves Moreau; Bart De Moor
Journal:  Nucleic Acids Res       Date:  2005-07-01       Impact factor: 16.971

6.  BLISS: binding site level identification of shared signal-modules in DNA regulatory sequences.

Authors:  Hailong Meng; Arunava Banerjee; Lei Zhou
Journal:  BMC Bioinformatics       Date:  2006-06-07       Impact factor: 3.169

7.  PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences.

Authors:  Saurabh Sinha; Mathieu Blanchette; Martin Tompa
Journal:  BMC Bioinformatics       Date:  2004-10-28       Impact factor: 3.169

8.  Functional evolution of a cis-regulatory module.

Authors:  Michael Z Ludwig; Arnar Palsson; Elena Alekseeva; Casey M Bergman; Janaki Nathan; Martin Kreitman
Journal:  PLoS Biol       Date:  2005-03-15       Impact factor: 8.029
  8 in total
  3 in total

1.  Regulatory modules function in a non-autonomous manner to control transcription of the mbp gene.

Authors:  Samar Dib; Eric Denarier; Nancy Dionne; Melissa Beaudoin; Hana H Friedman; Alan C Peterson
Journal:  Nucleic Acids Res       Date:  2010-12-03       Impact factor: 16.971

2.  Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs.

Authors:  Bartek Wilczynski; Norbert Dojer; Mateusz Patelak; Jerzy Tiuryn
Journal:  BMC Bioinformatics       Date:  2009-03-10       Impact factor: 3.169

3.  Proceedings of the 2008 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.

Authors:  Jonathan D Wren; Dawn Wilkins; James C Fuscoe; Susan Bridges; Stephen Winters-Hilt; Yuriy Gusev
Journal:  BMC Bioinformatics       Date:  2008-08-12       Impact factor: 3.169
  3 in total

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