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

No inputs are required.

Output

Writes the sequences in FASTA format to standard output.

Options

Option Parameter Description Default Behaviour
General Options
--bfilefile File containg a background model in background model format.
--seeds Seed for random number generator.
--minseqmin Minimum sequence length. The minimum sequence length is 50.
--maxseqmax Maximum sequence length. The maximum sequence length is 2,000.
--ordern Use Markov model of order n. 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.
--type0|1|2|3|4 Allowed types are:
  • 0 = protein (default)
  • 1 = DNA
  • 2 = codons
  • 3 = DNA without ambiguous characters
  • 4 = protein without ambigouous characters
Protein sequences are generated.