CONREAL web server: identification and visualization of conserved transcription factor binding sites

被引：20
|
作者：
Berezikov, E [1 ]
Guryev, V [1 ]
Cuppen, E [1 ]
机构：
[1] Netherlands Inst Dev Biol, Hubrecht Lab, NL-3584 CT Utrecht, Netherlands
来源：
NUCLEIC ACIDS RESEARCH | 2005年 / 33卷
关键词：
D O I：
10.1093/nar/gki378
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
The use of orthologous sequences and phylogenetic footprinting approaches have become popular for the recognition of conserved and potentially functional sequences. Several algorithms have been developed for the identification of conserved transcription factor binding sites (TFBSs), which are characterized by their relatively short and degenerative recognition sequences. The CONREAL (conserved regulatory elements anchored alignment) web server provides a versatile interface to CONREAL-, LAGAN-, BLASTZ- and AVID-based predictions of conserved TFBSs in orthologous promoters. Comparative analysis using different algorithms can be started by keyword without any prior sequence retrieval. The interface is available at http://conreal.niob.knaw.nl.
引用
收藏
页码：W447 / W450
页数：4
相关论文
共 50 条
  • [21] Identification of transcription factor binding sites using ATAC-seq
    Zhijian Li
    Marcel H. Schulz
    Thomas Look
    Matthias Begemann
    Martin Zenke
    Ivan G. Costa
    Genome Biology, 20
  • [22] Efficient Identification of Transcription Factor Binding Sites with a Graph Theoretic Approach
    Song, Jia
    Xu, Li
    Sun, Hong
    COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE, 2013, 2013
  • [23] TFinder: A Python']Python Web Tool for Predicting Transcription Factor Binding Sites
    Minniti, Julien
    Checler, Frederic
    Duplan, Eric
    da Costa, Cristine Alves
    JOURNAL OF MOLECULAR BIOLOGY, 2025, 437 (03)
  • [24] Web server for prediction of miRNAs and their precursors and binding sites
    P. S. Vorozheykin
    I. I. Titov
    Molecular Biology, 2015, 49 : 755 - 761
  • [25] Web server for prediction of miRNAs and their precursors and binding sites
    Vorozheykin, P. S.
    Titov, I. I.
    MOLECULAR BIOLOGY, 2015, 49 (05) : 755 - 761
  • [26] STarMir: a web server for prediction of microRNA binding sites
    Rennie, William
    Liu, Chaochun
    Carmack, C. Steven
    Wolenc, Adam
    Kanoria, Shaveta
    Lu, Jun
    Long, Dang
    Ding, Ye
    NUCLEIC ACIDS RESEARCH, 2014, 42 (W1) : W114 - W118
  • [27] Computational identification of conserved transcription factor binding sites upstream of genes induced in rat brain by transient focal ischemic stroke
    Pulliam, John V. K.
    Xu, Zhenfeng
    Ford, Gregory D.
    Liu, Cuimei
    Li, Yonggang
    Stovall, Kyndra C.
    Cannon, Virginetta S.
    Tewolde, Teclemichael
    Moreno, Carlos S.
    Ford, Byron D.
    BRAIN RESEARCH, 2013, 1495 : 76 - 85
  • [28] SeqTU: A Web Server for Identification of Bacterial Transcription Units
    Chen, Xin
    Chou, Wen-Chi
    Ma, Qin
    Xu, Ying
    SCIENTIFIC REPORTS, 2017, 7
  • [29] ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites
    Gonzalez, Santi
    Montserrat-Sentis, Barbara
    Sanchez, Friman
    Puiggros, Montserrat
    Blanco, Enrique
    Ramirez, Alex
    Torrents, David
    BIOINFORMATICS, 2012, 28 (06) : 763 - 770
  • [30] SeqTU: A Web Server for Identification of Bacterial Transcription Units
    Xin Chen
    Wen-Chi Chou
    Qin Ma
    Ying Xu
    Scientific Reports, 7
12345