Practical Sections on Pairwise Alignments

Dynamic Programming in C

• Write a C-function which reads a sequence (fasta-format) into an array:

    char * read_fasta_seq (char *FastaFile, 
                           char *id, int number);
  

  Go here for a description of the fasta format.
  
  
• Write a C-function which prints an alignment of two sequences on stdout
  presuming the two sequences including gaps have the same size:

    void print_alignment(char *id1, 
                         char *id2, 
                         char *seq1, 
                         char *seq2);
  

  
  
• Write a C-function to align two sequences:

    void align(char *seq1, 
               char *seq2, 
               char *seq1_gapped, 
               char *seq2_gapped, 
               char *matrix_file, 
               int gap_open_penalty, 
               int gap_extension_penalty);
  

  The commonly used score matrices PAM250 and BLOSUM62 can be found
  at the NCBI FTP Server (ncbi.nlm.nih.gov) in the directory /blast/matrices/.
  The new score matrix VT160 was introduced by Tobias Müller and Martin Vingron.

theory

---

Comments are very welcome.
luz@molgen.mpg.de