SYNOPSIS rselect - select a random set of sequences from a FASTA file. reps - extract exact k-word repeats based that occur in sequences grouped in different clusters. INSTALLATION You'll need GHC or possibly another Haskell system, and the Haskell bioinformatics library. The Makefile should work to build and install (by default to your home directory) the executables. USAGE rselect [-r] n [m] input.seq Selects n sequences from the file input.seq. If the optional m is given, this limits the selection to happen only from the first m sequences in the file, which may be more efficient. If -r is given, the sequences will be reoriented randomly. The selected sequences are written to standard output, so you probably want to redirect them to a file. reps k clustered.seq Generate a list of repeated k-words (or k-grams) found in the sequences. The sequences are expected to be on UniGene format, i.e. a FASTA file with #-initiated comments separating the clusters. A k-word is considered repeated if it is found in more than one of the clusters. reps k clustering.lst sequences.seq As above, but take a separate input clustering (and ignore any #'s in the sequences. The clustering should consist of one line per cluster, with each line containing the sequence identifier (first word after the initial '>' in the FASTA header). BUGS Do let me know about them, at ! HOMEPAGE http://malde.org/~ketil/