List of software and on-line resources for
GCB/CIS535
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 possible
varieties 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: (???)