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Home > Extras > Bioinformatics For Dummies® Bonus Material
Bioinformatics For Dummies® Bonus Material
By: Jean-Michel Claverie Ph.D., Cedric Notredame Ph.D.
 

[Bio FD Home][Ch.1][Ch.2][Ch.3][Ch.4][Ch.5][Ch.6][Ch.7][Ch.8][Ch.9][Ch.10][Ch.11][Ch.12][Ch.13][Ch.15]

Chapter 8: Comparing Two Sequences

Chapter 8 images

Various flavors of dot-plot programs

Name Used For Range URL Platforms
Dotlet Proteins, DNA 10,000 www.ch.embnet.org All
Dnadot Proteins, DNA 100,000 arbl.cvmbs.colostate.edu/molkit/dnadot/ All
Dotter Proteins, DNA 100,000 www.cgr.ki.se/cgr/groups/sonnhammer/Dotter.html Unix, Linux, Windows
Dottup Complete genomes, DNA >100,000 www.emboss.org Unix, Linux

Online pairwise alignment programs

Name URL Alignment Type
lalign www.ch.embnet.org/software/LALIGN_form.html Global/Local
lalign http://fasta.bioch.virginia.edu/fasta_www/plalign.htm Global/Local
alion fold.stanford.edu/alion/ Global/Local
align genome.cs.mtu.edu/align.html Global/Local
align www.ebi.ac.uk/emboss/align/ Global/Local
xenAliTwo www.soe.ucsc.edu/~kent/xenoAli/xenAliTwo.html Local for DNA
Blast2seqs www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html Local BLAST
Blast2seqs web.umassmed.edu/cgi-bin/BLAST/blast2seqs Local BLAST

Online pairwise alignment analyses

Name URL Function
lalnview www.expasy.ch/tools/sim-prot.html Visualization
prss www.ch.embnet.org/software/PRSS_form.html Evaluation
prss fasta.bioch.virginia.edu/fasta/prss.htm Evaluation
graph-align darwin.nmsu.edu/cgi-bin/graph_align.cgi Evaluation

 
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