List of software and on-line resources for GCB/CIS535

List of software and on-line resources forGCB/CIS535

GO:

http://www.geneontology.org/

http://www.ebi.ac.uk/GOA/

Gene Expression Software:

http://www.chem.agilent.com/Scripts/Generic.ASP?lPage=35082&indcol=Y&prodcol=Y

Linear regression

http://members.aol.com/johnp71/logistic.html

Pairwise sequence alignment:

http://www.ebi.ac.uk/emboss/align/index.html (Nucleotide and protein;local and global)

http://hto-13.usc.edu/software/seqaln/seqaln-query.html (align 2 sequences with all possiblevarieties of dynamic programming)

Multiple sequence alignment:

http://www.ebi.ac.uk/clustalw/index.html

http://bioweb.pasteur.fr/seqanal/interfaces/boxshade.html(pretty printing and shading of multiple alignments)

BLAST:

http://www.ncbi.nlm.nih.gov/BLAST/

http://www.paralign.org/ (A query using Smith-Waterman;can be used to compare with BLAST on speed vs. sensitivity)

Motif finding:

http://bayesweb.wadsworth.org/gibbs/gibbs.html(Gibbs)

http://atlas.med.harvard.edu/cgi-bin/alignace.pl (AlignAce)

http://meme.sdsc.edu/meme/website/meme.html(MEME)

Gene Prediction:

http://genes.mit.edu/GENSCAN.html

Promoter prediction: (????)

http://www.fruitfly.org/seq_tools/promoter.html(Neural Network)

http://genes.mit.edu/McPromoter.html(eukaryotic DNA)

UCSC genome browser:

http://www.genome.ucsc.edu/cgi-bin/hgGateway

VISTA:

http://gsd.lbl.gov/vista/index.shtml (Need JAVA2)

rVISTA:

http://gsd.lbl.gov/vista/rvista/submit.shtml

HMM:(???)

Expression data analysis:

http://www.ebi.ac.uk/microarray-srv/EP/cgi-bin/ep_ui.pl

Proteomics: (???)