Kent, W.J., Sugnet, C. W., Furey, T. S., Roskin, K.M., Pringle, T. H., Zahler, A. M., and Haussler, D. The Human Genome Browser at UCSC. Genome Res. 12(6), 996-1006 (2002).
Programa no publicat, cedit per cortesia de Robert Castelo.
The cgi interface to repeatmasker uses "cgi - model" Chenna Ramu et.al., (2000)cgi-model: CGI Programming Made Easy with Python. LINUX Journal, July 2000, 142-149.
Smit,AFA and Green,P RepeatMasker at http://repeatmasker.genome.washington.edu/cgi-bin/RM2_req.pl) or otherwise to Smit, AFA and Green, P., unpublished results.
RepeatMasker depends on the libraries provided by Repbase Update Jurka, J. Repbase Update: a database and an electronic journal of repetitive elements. Trends in Genetics 16(9):418-420 (2000).
Abril, J.F. and Guigó, R."gff2ps: visualizing genomic annotations." Bioinformatics, 16(8):743-744 (2000).
Copyright 1997-2005 Christopher Burge
GENSCAN is freely available for academic use. Executables are currently available for the following Unix platforms: Intel/Linux, Sun/Solaris, Intel/Solaris, SGI/Irix, DEC/Tru64, and IBM/AIX. Platforms not listed are not currently supported. To obtain a copy of GENSCAN for academic use, go to the academic license agreement web site and download the executable after completing the form.
For commercial use, contact Imelda Oropeza at the Stanford University Office of Technology Licensing.
The current version of geneid has been written by Enrique Blanco and Roderic Guigó. The parameter files have been constructed by Genis Parra and Francisco Camara. With contributions from Josep F.Abril, Moises Burset and Xavier Messeguer.
Solovyev, V.V., Salamov, A.A., and Lawrence, C.B. 1995. Identification of human gene structure using linear discriminant functions and dynamic programming. In Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology (ed. C. Rawling et al.), pp. 367-375. AAAI Press, Menlo Park, CA.
Programa elaborat per Josep F. Abril.
Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences.J Comput Biol. 2000 Feb-Apr;7(1-2):203-14.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ.Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.Nucleic Acids Res. 1997 Sep 1;25(17):3389-402.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ.Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389-402.
Quevillon E., Silventoinen V., Pillai S., Harte N., Mulder N., Apweiler R., Lopez R. (2005). InterProScan: protein domains identifier. Nucleic Acids Research 33: W116-W120
Higgins D., Thompson J., Gibson T.Thompson J.D., Higgins D.G., Gibson T.J.(1994).CLUSTAL W: improving the sensitivity of progressivemultiple sequence alignment through sequence weighting,position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
Durant tot el treball hem elaborat un report.
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