ccmbweb.ccv.brown.edu

Brown University Center for Computational Molecular Biology

BALSA - Bayesian Algorithm for Local Sequence Alignment. RNAG - Block Gibbs Sampler for RNA Prediction. EBIR - Exact Bayesian Inference in Regression. Experimental Design and Reproducibility. Phyloscan - search for sequence motifs in intergenic regions. Effective - Effective Species Count. Significance of Pairwise Sequence Alignment Scores. Software for Probabilistic Sequence Alignment of Stratigraphic Records. Last modified: Fri Oct 28 12:48:14 EDT 2011.

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Brown University Center for Computational Molecular Biology | ccmbweb.ccv.brown.edu Reviews

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BALSA - Bayesian Algorithm for Local Sequence Alignment. RNAG - Block Gibbs Sampler for RNA Prediction. EBIR - Exact Bayesian Inference in Regression. Experimental Design and Reproducibility. Phyloscan - search for sequence motifs in intergenic regions. Effective - Effective Species Count. Significance of Pairwise Sequence Alignment Scores. Software for Probabilistic Sequence Alignment of Stratigraphic Records. Last modified: Fri Oct 28 12:48:14 EDT 2011.

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2 bayesian phylogenetic footprinting

3 gibbs motif sampler

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Brown University Center for Computational Molecular Biology | ccmbweb.ccv.brown.edu Reviews

https://ccmbweb.ccv.brown.edu

BALSA - Bayesian Algorithm for Local Sequence Alignment. RNAG - Block Gibbs Sampler for RNA Prediction. EBIR - Exact Bayesian Inference in Regression. Experimental Design and Reproducibility. Phyloscan - search for sequence motifs in intergenic regions. Effective - Effective Species Count. Significance of Pairwise Sequence Alignment Scores. Software for Probabilistic Sequence Alignment of Stratigraphic Records. Last modified: Fri Oct 28 12:48:14 EDT 2011.

INTERNAL PAGES

ccmbweb.ccv.brown.edu

1

Bayesian Algorithm for Local Sequence Alignment

http://ccmbweb.ccv.brown.edu/balsa.html

BALSA: Bayesian Algorithm for Local Sequence Alignment. View an annotated example. Browse the BALSA Pairwise Sequence Alignment User Manual. Run the BALSA Pairwise Sequence Alignment Program. BALSA is described in:. Webb, B. J., J. S. Liu, et al. (2002). BALSA: Bayesian algorithm for local sequence alignment. Webb-Robertson, B. J., L. A. McCue, et al. (2008). Measuring Global Credibility with Application to Local Sequence Alignment.

2

The Gibbs Motif Sampler Homepage

http://ccmbweb.ccv.brown.edu/gibbs/gibbs.html

The Gibbs Motif Sampler Homepage. Welcome to the Gibbs Motif Sampler Homepage. The Gibbs Motif Sampler will allow you to identify motifs, conserved regions, in DNA or protein sequences. This software was developed by Eric C. Rouchka and Bill Thompson based on work by C. E. Lawrence, J. S. Liu, L. A. McCue, A. F. Neuwald, L. A. Newberg and others (References). Gibbs version 3.1 source and binaries for Linux, MS Windows (using Cygwin), Solaris, Solaris.x86 and MAC OS-X are available here.

3

Download the HMM Match Software

http://ccmbweb.ccv.brown.edu/cgi-bin/download_HMM_Match.pl

Download Software for Probabilistic Sequence Alignment of Stratigraphic Records. If this software is used in a publication, please cite Lin et al. "Probabilistic sequence alignment of stratigraphic records." doi:10.1002/2014PA002713. The paper can be downloaded here. Please enter you name and e-mail address. E-mail Address (optional) :.

4

Bayesian Phylogenetic Footprinting

http://ccmbweb.ccv.brown.edu/cgi-bin/bayes_align_ccmb.pl

Please acknowledge the program authors on any publication of scientific results based in part on use of the program and cite the article in which the program was described (Zhu, J. Liu, J.S. Lawrence, C.E. Bayesian adaptive sequence alignment algorithms. Bioinformatics. The Bayes Aligner Source (GPL). Enter your email address. You will be contacted by email when your job completes. Please enter Query sequence:(FASTA format). Or click on Browse button to upload a FASTA file.

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Brown University Center for Computational Molecular Biology

BALSA - Bayesian Algorithm for Local Sequence Alignment. RNAG - Block Gibbs Sampler for RNA Prediction. EBIR - Exact Bayesian Inference in Regression. Experimental Design and Reproducibility. Phyloscan - search for sequence motifs in intergenic regions. Effective - Effective Species Count. Significance of Pairwise Sequence Alignment Scores. Software for Probabilistic Sequence Alignment of Stratigraphic Records. Last modified: Fri Oct 28 12:48:14 EDT 2011.

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