gendb

Usage: gendb [options] <numseqs>

Description:

gendb generates the specified number of sequences using a Markov model. The sequence lengths are selected uniformly at random within the range specified by --minseq and --maxseq.

Input:

• None

Output:

• Writes the sequences in FASTA format to stdout.

Options:

• --bfile <file> - File containg a background model in background model format.
• --seed <n> - Seed for random number generator.
• --minseq <n> - Minimum sequence length. Default value: 50.
• --maxseq <n> - Maximum sequence length. Default value: 2000.
• --order <n> - Use Markov model of order <n>. Default value: the order of the background model if one is provided, otherwise 0.
• --dummy - Print a "dummy" sequence record before the generated sequences. The "dummy" sequence record is a a FASTA header line listing the gendb parameters but not followed by any sequence lines.
• --type [0|1|2|3|4] - The type of sequence to generate. Allowed types are:
  • 0 = protein (default)
  • 1 = DNA
  • 2 = codons
  • 3 = DNA without ambiguous characters
  • 4 = protein without ambigouous characters

Bugs: None known.

Author: Tim Bailey