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

Provided by: patman_1.2.2+dfsg-6build1_amd64

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>