Burge Lab Software

A repository of bioinformatics software and databases developed in the Chris Burge lab at MIT

All software produced by our lab is available (by download or by request from the author) free of charge by academic and other non-profit researchers. For those who prefer not to install the software on their own computer, most software is also available through web servers.

Commercial use of the Genscan and GenomeScan gene identification programs requires a license from Stanford University. For information about how to obtain a license, please contact Imelda Oropeza (imelda.oropeza at stanford dot edu).

This site is under development, so please check back regularly for updates.

Software	Version	Description	Author(s)	Reference(s)	Web Server(s)	How to Obtain Source Code/Binaries/Data Files
ACEScan	1.0	Algorithm for prediction of conserved alternatively spliced exons from pairs of conserved mouse/human exons	Gene Yeo, Chris Burge	Yeo, G., Van Nostrand, E., Holste, D., Poggio, T. and Burge, C. B. (2005). Identification and analysis of alternative splicing events conserved in human and mouse. Proc. Natl. Acad. Sci. USA 102, 2850-2855.	MIT ACEScan Server	Contact Gene Yeo (geneyeo at salk dot edu)
DiCodonShuffle, CodonShuffle, DiShuffle	1.0	Algorithms for generating random control mRNAs that preserve dinucleotide content and/or synonymous codon usage of a native mRNA sequence	Luba Katz, Chris Burge	Katz, L. and Burge, C. B. (2003). Widespread selection for local RNA structure in coding regions of bacterial genes. Genome Res. 13, 2042-2051.	N/A	Anonymous ftp to hollywood.mit.edu cd pub get mrnashuffle.tar.gz (gzipped tar file - read README file for further instructions)
ExonScan	1.0	Algorithm for simulating the RNA splicing pattern of a primary transcript sequence	Michael Rolish, Chris Burge	Wang, Z., Rolish, M. E., Yeo, G., Tung, V., Mawson, M. and Burge, C. B. (2004). Systematic identification and analysis of exonic splicing silencers. Cell 119, 831-845.	MIT ExonScan Web Server	Contact Chris Burge (cburge at mit dot edu)
GENSCAN	1.0	Algorithm for ab initio prediction of complete gene structures in vertebrate, Drosophila and plant genomic sequences	Chris Burge	Burge, C. and Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78 - 94.	MIT GENSCAN server	License/Download Instructions
GenomeScan	1.0	Algorithm for prediction of complete gene structures in vertebrate genomic sequences integrating primary sequence and protein sequence similarity information	Ru-Fang Yeh, Chris Burge	Yeh, R.-F., Lim, L. P. and Burge, C. B. (2001). Computational inference of homologous gene structures in the human genome. Genome Res. 11, 803-816.	MIT GenomeScan Server	Contact Chris Burge (cburge at mit dot edu)
Hollywood	1.0	Comparative genomic relational database of mammalian alternative splicing	Dirk Holste, George Huo, Vivian Tung, Chris Burge	Holste, D., Huo, G., Tung, V. and Burge, C. B. (2006). HOLLYWOOD: a comparative relational database of alternative splicing. Nucl. Acids Res. 34, D56-62.	MIT Hollywood Server	Anonymous ftp to hollywood.mit.edu cd pub/hollywood.freeze.20060101 get and read the README file for further instructions
IntronScan	1.0	Algorithm for simulating splicing of short introns in various organisms	Lee Lim, Chris Burge	Lim, L. P. and Burge, C. B. (2001). A computational analysis of sequence features involved in recognition of short introns. Proc. Natl. Acad. Sci. USA 98, 11193 11198.	N/A	Anonymous ftp to hollywood.mit.edu cd pub get intronscan.tar.gz (gzipped tar file - read README file for further instructions)
MaxEnt	1.0	Algorithms for derivation and scoring of constrained-marginal maximum entropy distributions, with applications to 5' and 3' splice sites	Gene Yeo, Chris Burge	Yeo, G. and Burge, C. B. (2004). Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J. Comp. Biol. 11, 377-394.	MIT MaxEnt Build Server MIT MaxEnt Splice Site Scoring Server	Contact Gene Yeo (geneyeo at salk dot edu)
MiRScan	1.0	Algorithm for predicting microRNA genes from pairs of conserved sequences with potential to form RNA foldbacks	Lee Lim, Chris Burge, David Bartel	Lim, L. P., Glasner, M. E., Yekta, S., Burge, C. B. and Bartel, D. P. (2003). Vertebrate microRNA genes. Science 299, 1540. Lim, L. P., Lau, N. C., Weinstein, E. G., Abdelhakim, A., Yekta, S., Rhoades, M. W., Burge, C. B. and Bartel, D. P. (2003). The microRNAs of Caenorhabditis elegans. Genes & Dev. 17, 977-990.	MIT MiRScan Server	Anonymous ftp to hollywood.mit.edu cd pub get miRscan.tar.gz (gzipped tar file - read README file for further instructions)
MISO	1.0	Computational method for quantitating isoform expression and detecting differentially expressed isoforms.	Yarden Katz, Eric T. Wang, Edoardo M. Airoldi Christopher B. Burge	Katz Y, Wang ET, Airoldi EM, Burge CB. (2010). Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nature Methods (in press).	MISO website	Download MISO
Pictogram	1.0	Tool for displaying a sequence motif based on a set of aligned DNA or RNA sequences.	Chris Burge	Burge, C. B., Tuschl, T. H. and Sharp, P. A. (1999). Splicing of precursors to mRNAs by the spliceosomes. In Gesteland, R. F., Cech, T. and Atkins, J. F., eds. The RNA World, 2nd Ed., Cold Spring Harbor Laboratory Press, Plainview, NY, pp. 525-560.	MIT Pictogram Server	Anonymous ftp to hollywood.mit.edu cd pub get pictogram.tar.gz (gzipped tar file - read README file for further instructions)
PLATA	1.0	Software for probe level alternative transcript analysis of Affymetrix all-exon array data	Rickard Sandberg	Sandberg, R., Neilson, J. R., Sarma, A., Sharp, P. A. and Burge, C. B. (2008). Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites. Science 320, 1643-1646.	N/A	PLATA software download site
PVSA	1.0	Software package for identification of coevolutionary networks.	Xinshu (Grace) Xiao, Chris Burge	Xiao, X., Wang, Z., Jang, M. and Burge, C. B. (2007). Coevolutionary networks of splicing cis-regulatory elements. PNAS 47, 18583-18588.	N/A	Anonymous ftp to hollywood.mit.edu cd pub get pvsa.tar.gz (gzipped tar file - read readme.txt file for further instructions)
TargetRank	1.0	Algorithm for ranking conserved and non-conserved microRNA targets and siRNA off-targets.	Cydney Nielsen, Chris Burge	Nielsen, C.B., Shomron, N., Sandberg, R., Hornstein, E., Kitzman, J. and Burge, C.G. (2007). Determinants of targeting by endogeno us and exogenous microRNAs and siRNAs. RNA 13, 1894-1910.	MIT TargetRank Server	Contact Cydney Nielsen (cydney at mit dot edu)
TargetScan(S)	1.0	Algorithm for prediction of microRNA targets based on mRNA sequence conservation in multiple species	Ben Lewis, Chris Burge, David Bartel	Lewis, B. P., Shih, I-h., Jones-Rhoades, M. W., Bartel, D. P. and Burge, C. B. (2003). Prediction of mammalian microRNA targets. Cell 115, 787-798. (TargetScan) Lewis, B. P., Burge, C. B. and Bartel, D. P. (2005). Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15-20. (TargetScanS)	targetscan.org	Contact Ben Lewis (benlewis at mit dot edu) or wibr-bioinformatics at wi dot mit dot edu
UNCOVER	1.0	Algorithm for predicting conserved alternatively spliced exons (and retained introns) in orthologous intron pairs	Uwe Ohler, Chris Burge	Ohler, U., Shomron, N. and Burge, C. B. (2005). Recognition of unknown conserved alternatively spliced exons. PLoS Comput. Biol. 1, 113-122.	N/A	Contact Uwe Ohler (uwe dot ohler at duke dot edu)

Software

Version

Description

Author(s)

Reference(s)

Web Server(s)

How to Obtain Source Code/Binaries/Data Files

ACEScan

1.0

Algorithm for prediction of conserved alternatively spliced exons from pairs of conserved mouse/human exons

Gene Yeo, Chris Burge

Yeo, G., Van Nostrand, E., Holste, D., Poggio, T. and Burge, C. B. (2005). Identification and analysis of alternative splicing events conserved in human and mouse. Proc. Natl. Acad. Sci. USA 102, 2850-2855.

MIT ACEScan Server

Contact Gene Yeo (geneyeo at salk dot edu)

DiCodonShuffle, CodonShuffle, DiShuffle

1.0

Algorithms for generating random control mRNAs that preserve dinucleotide content and/or synonymous codon usage of a native mRNA sequence

Luba Katz, Chris Burge

Katz, L. and Burge, C. B. (2003). Widespread selection for local RNA structure in coding regions of bacterial genes. Genome Res. 13, 2042-2051.

N/A

Anonymous ftp to hollywood.mit.edu

cd pub

get mrnashuffle.tar.gz

(gzipped tar file - read README file for further instructions)

ExonScan

1.0

Algorithm for simulating the RNA splicing pattern of a primary transcript sequence

Michael Rolish, Chris Burge

Wang, Z., Rolish, M. E., Yeo, G., Tung, V., Mawson, M. and Burge, C. B. (2004). Systematic identification and analysis of exonic splicing silencers. Cell 119, 831-845.

MIT ExonScan Web Server

Contact Chris Burge (cburge at mit dot edu)

GENSCAN

1.0

Algorithm for ab initio prediction of complete gene structures in vertebrate, Drosophila and plant genomic sequences

Chris Burge

Burge, C. and Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78 - 94.

MIT GENSCAN server

License/Download Instructions

GenomeScan

1.0

Algorithm for prediction of complete gene structures in vertebrate genomic sequences integrating primary sequence and protein sequence similarity information

Ru-Fang Yeh, Chris Burge

Yeh, R.-F., Lim, L. P. and Burge, C. B. (2001). Computational inference of homologous gene structures in the human genome. Genome Res. 11, 803-816.

MIT GenomeScan Server

Contact Chris Burge (cburge at mit dot edu)

Hollywood

1.0

Comparative genomic relational database of mammalian alternative splicing

Dirk Holste, George Huo, Vivian Tung, Chris Burge

Holste, D., Huo, G., Tung, V. and Burge, C. B. (2006). HOLLYWOOD: a comparative relational database of alternative splicing. Nucl. Acids Res. 34, D56-62.

MIT Hollywood Server

Anonymous ftp to hollywood.mit.edu

cd pub/hollywood.freeze.20060101

get and read the README file for further instructions

IntronScan

1.0

Algorithm for simulating splicing of short introns in various organisms

Lee Lim,
Chris Burge

Lim, L. P. and Burge, C. B. (2001). A computational analysis of sequence features involved in recognition of short introns. Proc. Natl. Acad. Sci. USA 98, 11193 11198.

N/A

Anonymous ftp to hollywood.mit.edu

cd pub

get intronscan.tar.gz

(gzipped tar file - read README file for further instructions)

MaxEnt

1.0

Algorithms for derivation and scoring of constrained-marginal maximum entropy distributions, with applications to 5' and 3' splice sites

Gene Yeo, Chris Burge

Yeo, G. and Burge, C. B. (2004). Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J. Comp. Biol. 11, 377-394.

MIT MaxEnt Build Server

MIT MaxEnt Splice Site Scoring Server

Contact Gene Yeo (geneyeo at salk dot edu)

MiRScan

1.0

Algorithm for predicting microRNA genes from pairs of conserved sequences with potential to form RNA foldbacks

Lee Lim,
Chris Burge,
David Bartel

Lim, L. P., Glasner, M. E., Yekta, S., Burge, C. B. and Bartel, D. P. (2003). Vertebrate microRNA genes. Science 299, 1540.

Lim, L. P., Lau, N. C., Weinstein, E. G., Abdelhakim, A., Yekta, S., Rhoades, M. W., Burge, C. B. and Bartel, D. P. (2003). The microRNAs of Caenorhabditis elegans. Genes & Dev. 17, 977-990.

MIT MiRScan Server

Anonymous ftp to hollywood.mit.edu

cd pub

get miRscan.tar.gz

(gzipped tar file - read README file for further instructions)

MISO

1.0

Computational method for quantitating isoform expression and detecting differentially expressed isoforms.

Yarden Katz,
Eric T. Wang,
Edoardo M. Airoldi
Christopher B. Burge

Katz Y, Wang ET, Airoldi EM, Burge CB. (2010). Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nature Methods (in press).

MISO website

Download MISO

Pictogram

1.0

Tool for displaying a sequence motif based on a set of aligned DNA or RNA sequences.

Chris Burge

Burge, C. B., Tuschl, T. H. and Sharp, P. A. (1999). Splicing of precursors to mRNAs by the spliceosomes. In Gesteland, R. F., Cech, T. and Atkins, J. F., eds. The RNA World, 2nd Ed., Cold Spring Harbor Laboratory Press, Plainview, NY, pp. 525-560.

MIT Pictogram Server

Anonymous ftp to hollywood.mit.edu

cd pub

get pictogram.tar.gz

(gzipped tar file - read README file for further instructions)

PLATA

1.0

Software for probe level alternative transcript analysis of Affymetrix all-exon array data

Rickard Sandberg

Sandberg, R., Neilson, J. R., Sarma, A., Sharp, P. A. and Burge, C. B. (2008). Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites. Science 320, 1643-1646.

N/A

PLATA software download site

PVSA

1.0

Software package for identification of coevolutionary networks.

Xinshu (Grace) Xiao, Chris Burge

Xiao, X., Wang, Z., Jang, M. and Burge, C. B. (2007). Coevolutionary networks of splicing cis-regulatory elements. PNAS 47, 18583-18588.

N/A

Anonymous ftp to hollywood.mit.edu

cd pub

get pvsa.tar.gz

(gzipped tar file - read readme.txt file for further instructions)

TargetRank

1.0

Algorithm for ranking conserved and non-conserved microRNA targets and siRNA off-targets.

Cydney Nielsen, Chris Burge

Nielsen, C.B., Shomron, N., Sandberg, R., Hornstein, E., Kitzman, J. and Burge, C.G. (2007). Determinants of targeting by endogeno us and exogenous microRNAs and siRNAs. RNA 13, 1894-1910.

MIT TargetRank Server

Contact Cydney Nielsen (cydney at mit dot edu)

TargetScan(S)

1.0

Algorithm for prediction of microRNA targets based on mRNA sequence conservation in multiple species

Ben Lewis, Chris Burge, David Bartel

Lewis, B. P., Shih, I-h., Jones-Rhoades, M. W., Bartel, D. P. and Burge, C. B. (2003). Prediction of mammalian microRNA targets. Cell 115, 787-798. (TargetScan)

Lewis, B. P., Burge, C. B. and Bartel, D. P. (2005). Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15-20. (TargetScanS)

targetscan.org

Contact Ben Lewis (benlewis at mit dot edu) or

wibr-bioinformatics at wi dot mit dot edu

UNCOVER

1.0

Algorithm for predicting conserved alternatively spliced exons (and retained introns) in orthologous intron pairs

Uwe Ohler, Chris Burge

Ohler, U., Shomron, N. and Burge, C. B. (2005). Recognition of unknown conserved alternatively spliced exons. PLoS Comput. Biol. 1, 113-122.

N/A

Contact Uwe Ohler (uwe dot ohler at duke dot edu)

Christopher Burge Laboratory
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Burge Lab Software A repository of bioinformatics software and databases developed in the Chris Burge lab at MIT All software produced by our lab is available (by download or by request from the author) free of charge by academic and other non-profit researchers. For those who prefer not to install the software on their own computer, most software is also available through web servers. Commercial use of the Genscan and GenomeScan gene identification programs requires a license from Stanford University. For information about how to obtain a license, please contact Imelda Oropeza (imelda.oropeza at stanford dot edu). This site is under development, so please check back regularly for updates.