CS 5124: Algorithms in Bioinformatics

Fall Semester, 2004
Other Resources

Basic Course Information

• Our textbook:

  • Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology by Daniel M. Gusfield, Cambridge University Press, 1998

• Find out what is on reserve in Newman Library.

Related Courses

• See the web site for the companion course --- PPWS 5314: Biological Paradigms for Bioinformatics.

• You can see the Algorithms in Bioinformatics web sites for Fall, 2003, Fall, 2002, Fall, 2001, and Fall, 2000.

• Also see the web site for the course CS 6104: Computational Biology.

• A self-study course in Perl was taught during Spring, 2001; Perl will be a useful tool for the homework in CS 5124.

NCBI: National Center for Biotechnology Information

• NCBI: National Center for Biotechnology Information

• BLAST searching in NCBI databases

• Retrieve stand-alone BLAST executables.

• The NCBI Software Development Toolkit includes source code for tools developed at NCBI, including source code for their version of BLAST.

• NCBI references for BLAST and PSI-BLAST

• Search for relevant journal articles in PubMed, the bibliographic database of the National Library of Medicine.

Biological Information Sources

• Some resources related to the genetic code are available.

Additional Course Materials

• Incremental String Comparison. Gad M. Landau, Eugene W. Myers, Jeanette P. Schmidt.
  SIAM Journal on Computing, Volume 27, Number 2, 1998, pp. 557-582.

Biological Sequence Comparison

• Some resourses on protein scoring matrices are available.

• Some resourses on FASTA are available.

• Some resourses on BLAST are available.

• Some resourses on analyzing sequence statistics and algorithms are available.