FCODE - Preliminary Profile/Sequence Search Code

FCODE is a preliminary version of the PSSMsearch program, which will determine the optimal local alignment of a profile and sequence using techniques that require only linear storage space.

Files you may copy include:

• Makefile, the make file;
• main.f, the main program.
• getwrd.f, gets the next word from a line of text.
• lastch.f, various string manipulation routines.
• local_align.f90, determines the optimal local alignment of a profile and string
• nuclab.f, sets integer labels for nucleotides.
• profile_score.f90, scores the match of a pair of profile and string entries.
• protab.f, sets integer labels for proteins.
• readseq.f, reads a sequence in a variety of formats.
• translate.f, the main program.
• ps_lg_align.f90, a sample sequence specification;
• profile.txt, a sample profile specification.
• my.seq, a sample sequence specification;
• pssm.out, the output of a run of the program on the sample data.

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