Abstract:
:RegAnalyst is a user-friendly web interface that integrates MoPP (Motif Prediction Program), MyPatternFinder (pattern detection tool) and MycoRegDB (mycobacterial promoter and regulatory elements database). Since motif discovery is a challenging task, numerous tools have been developed over the past few years. Strikingly, the existing programs were not successful in detecting the known consensus in all mycobacterial (epitomizing degenerate) datasets even in the absence of noise and their performance was further reduced in the presence of noise. Consequently, MoPP, a de novo and greedy (for degeneracy) 'inexact' word-based tool that is tailored to enumerate significantly conserved degenerate oligonucleotide motifs was developed. Benchmarking on datasets from MycoRegDB and SCPD (http://rulai.cshl.edu/SCPD/) indicate that MoPP (i) consistently outperforms other motif discovery tools on highly degenerate as well as less degenerate datasets and (ii) successfully detects completely degenerate motifs (with no two instances of a pattern being exactly the same) even in the presence of noise. We have also developed another accessory program, MyPatternFinder, that scans a given sequence or genome to find exact or approximate matches to a query motif of any length identified by MoPP or any other user-defined motif. RegAnalyst will be a valuable tool for in silico analysis of regulatory networks and can be accessed at http://www.nii.ac.in/~deepak/RegAnalyst.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Sharma D,Mohanty D,Surolia Adoi
10.1093/nar/gkp388subject
Has Abstractpub_date
2009-07-01 00:00:00pages
W193-201issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gkp388journal_volume
37pub_type
杂志文章abstract::Owing to their great potentials in genetic code extension and the development of nucleic acid-based functional nanodevices, DNA duplexes containing HgII-mediated base pairs have been extensively studied during the past 60 years. However, structural basis underlying these base pairs remains poorly understood. Herein, w...
journal_title:Nucleic acids research
pub_type: 杂志文章
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks056
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
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doi:10.1093/nar/7.3.611
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
pub_type: 杂志文章
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journal_title:Nucleic acids research
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更新日期:2011-09-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr455
更新日期:2011-09-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
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journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:1986-10-10 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx388
更新日期:2017-07-07 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq602
更新日期:2010-09-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1152
更新日期:2015-01-01 00:00:00
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
pub_type: 杂志文章,评审
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journal_title:Nucleic acids research
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更新日期:2012-01-01 00:00:00
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
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更新日期:2017-11-02 00:00:00
abstract::The transcription factor HIV-TF1, which binds to a region about 60 bp upstream from the enhancer of the human immunodeficiency virus-1 (HIV-1), was purified from human B cells. HIV-TF1 had a molecular weight of 39,000. Binding of HIV-TF1 to the HIV long terminal repeat (LTR) activated transcription from the HIV promot...
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更新日期:1991-09-11 00:00:00