ReAlignerV

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HMO_5169

NOTICE

• Jun 20, 2010: ReAlignerVR (RAVR.1.1.1): Derived from RAV.8.1.4 for aligning 3'UTR sequences (RAVR.1.1.1), not for on-web. Outline of RAVR.1.1.1.
• Mar 16, 2010: ReAlignerV command-line version minor update (RAV.8.1.5), not for on-web. RAV.8.1.5 revision detail.
• Feb 22, 2008: ReAlignerV article was published in BMC Bioinformatics. 9(1):112, Iwama H. et al.
• Dec 9, 2007: ReAlignerV has been up-versioned (RAV.8.1.4), for both on-web and command-line programs.
• Dec 9, 2007: ReAlignerV Test dataset has been renewed.
• Nov. 5, 2007: ReAlignerV services have been completely restarted, following completion of the campus network overhaul.

ReAlignerV is an alignment tool focusing on genomic nucleotide sequences upstream of genes.
ReAlignerV integrates TRANSFAC(R) Match(TM) results to detect the conserved TFBSs.
ReAlignerV is robust against transposable element insertions.
ReAlignerV integrates RepeatMasker annotation results, which facillitates detection of conserved TFBSs located within the transposable elements.

ReAlignerV Web Services

Start-Up Instructions for Web ReAlignerV

Please make sure that the sequences to be submitted are NOT reverse-strand sequences! (Details)

• 2-species ReAlignerV
  ------------------------------> Test dataset
  
• 3-species ReAlignerV
  ------------------------------> Test dataset
  

FAQ

Command-Line ReAlignerV

• Download command-line ReAlignerV (RAV.8.1.4) and the Test dataset.
• Instructions --> PDF

If you publish results obtained by using ReAlignerV either through web or by locally installed settings,
please cite BMC Bioinformatics. 9(1):112, Iwama H. et al.

REALIGNER

REALIGNER is an aligner implemented in ReAlignerV.
Download REALIGNER and the Test Set.
Instructions --> PDF
If you publish results obtained by using REALIGNER, please cite Iwama H & Gojobori T, PNAS 2004, 101(49):17156-17161.

Contact about ReAlignerV to the author Hisakazu IWAMA, and about server technical problems to Yukio HORI.

Construction of ReAlignerV program and web services were supported partly by NIG Cooperative Research Program (2007-A57) and partly by Nankai Scholarship Foundation.

June 2008 through March 2010, ReAligerV program and web services, and construction of ReAlignerVR had been supported by A Grant-in-Aid for Scientific Research (KAKENHI) 20570222 of The Ministry of Education, Culture, Sports, Science and Technology (MEXT).

Since April 2011, ReAlignerV program, its web services, and ReAlignerVR program have been supported by A Grant-in-Aid for Scientific Research (KAKENHI) 23570273 of The Ministry of Education, Culture, Sports, Science and Technology (MEXT).

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