Ubuntu Manpage: PatMaN - search for approximate patterns in DNA libraries

NAME

       PatMaN - search for approximate patterns in DNA libraries

SYNOPSIS

       patman [ option | file ... ]

DESCRIPTION

       PatMaN searches for (small) patterns in (huge) DNA databases, allowing for some mismatches and optionally
       gaps.   Patterns  and  databases are read from one or more fasta(5) files listed as non-option arguments,
       depending on whether the -D or -P option last preceded them, and matched against each other.  The  output
       of PatMaN is a table containing one line for each match, consisting of tab-separated fields:

       •   name of database sequence,

       •   name of pattern,

       •   position of first matched base in database sequence, the sequence's beginning has position 1,

       •   position of last matched base in database sequence,

       •   strand (+ for literal match, - for reverse complement),

       •   edit distance (number of mismatches plus number of gaps).

OPTIONS

-V, --version
Print version number and exit.

-e num, --edits num
Allow up to num mismatches and/or gaps per match.

-g num, --gaps num
Allow up to num gaps per match. Note that gaps count as mismatches, too, so the -e option should
always be set at least as high as the -g option. Allowing many gaps can incur a considerable
computational cost.

-D, --databases
Treat the following files as database. Databases must be in fasta(5) format. Multiple database
files, including "-" for standard input, are allowed and are read in turn.

-P, --patterns
Treat the following files as patterns. Pattern files must be in fasta(5) format. Multiple
pattern files, including "-" for standard input, are allowed and are all read before touching the
databases.

-o file, --output file
Redirect output to file. The file name "-" causes output to be written to stdout, which is also
the default

-a, --ambicodes
Activate the interpretation of ambiguity codes in patterns. This results in the expansion of any
pattern with ambiguity codes into multiple patterns which can match independently. Compare
Unknown Nucleotides below.

-s, --singlestrand
Deactivate matching of reverse-complements. Normally, PatMaN will try to match patterns both
literally and after reverse-complementing them, with this option set, only straight forward
matches are considered.

-p num, --prefetch num
Causes num pointers to be prefetched in advance. This feature can improve performance, if PatMaN
has been compiled for a processor architecture that supports prefetching. The optimum value for
your particular setup has to be determined empirically, but the default should be reasonably good.

-l len, --min-length len
Only consider patterns with a length of at least len. Use this if your pattern collection
contains short sequences that you don't want lots of possible matches reported for.

-x num, --chop3 num
Cut off num bases from the 3' end of each pattern. Use this for patterns with damaged, edited,
etc. 3' ends that should be ignored. The chopped bases are neither matched nor included in the
reported match regions.

-X num, --chop5 num
Cut off num bases from the 5' end of each pattern. Use this for patterns with damaged, edited,
etc. 5' ends that should be ignored. The chopped bases are neither matched nor included in the
reported match regions.

-A, --adenine-hack
Allow adenine to be ignored in patterns. This is essentially equivalent to not counting gaps in
the database, as long as it was an A that was gapped. Using -A can be computationally extremely
expensive, both in terms of memory and time consumed.

-q, --quiet
Suppress warnings (about unrecognized characters in input sequences or missing input files). Even
without -q, at most one such warning is given per run.

-v, --verbose
Prints additional progress information to stderr.

-d flags, --debug flags
Sets debugging flags to flags.Flags may be the logical OR of any of the following values, each of
which causes some output to appear on stderr. Some of the values may only work if PatMaN has been
compiled in debug mode. The default value is 1.

1 Print warnings. Equivalent to not setting -q.

2 Print progress information. Equivalent to setting -v.

4 Dump the suffix trie of the patterns. Only available in debug build.

8 Count number of visited nodes and print that number in each iteration. Only available in debug
build.

16 Print total number of nodes fetched from memory after completing all databases.

32 Output database sequence while it is being matched.

NOTES

Non-Option Arguments
Non-option arguments (bare filenames) are either treated as database or pattern files, depending on
whether the -D or -P option was the the last that occurred before the filename. If neither -D nor -P was
given, file names are treated as pattern files. If no database was given, it is instead read from
standard input. Standard input can be explicitly given as either a database or a pattern file by using
the filename "-". A warning is given if standard input is selected implicitly as database, an error
message is given if no pattern files have been named at all.

Gapped Matching
Allowing gaps often causes overlapping matches of single patterns at almost the same position. PatMaN
makes no attempt to filter these redundant matches. Also note that allowing many gaps, and especially
allowing an arbitrary amount of gaps through the -A hack can slow down PatMaN considerably and cause it
to produce enormous amounts of output. The use of some sorty of post-processor to filter these is highly
recommended.

Unknown Nucleotides
Unknown nucleotides are most often encoded by the letter N. If the --ambicodes option is not given, Ns
in patterns are interpreted as unknown nucleotides and can never match without penalty. If --ambicodes
is given, Ns in patterns are expanded just like the other amibuguity codes, and effectively work as
wildcards. Unknown nucleotides can still be encoded by an X and will never match anything. The database
is treated differently in that anything other than A, C, G, T and U, including ambiguity codes, is
treated as unknown and can never match without penalty.

FILES

       /etc/popt
              The system wide configuration file for popt(3).  PatMaN identifies itself as "patman" to popt.

       ~/.popt
              Per user configuration file for popt(3).

BUGS

       None known.

AUTHOR

       Kay Pruefer <pruefer@eva.mpg.de>
       Udo Stenzel <udo_stenzel@eva.mpg.de>