--- name: "patman" section: "1" platform: "linux" package: "patman" version: "1.2.2+dfsg-8+b1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/patman" --- # patman(1) 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)](/popt/3.md). **PatMaN** identifies itself as "patman" to popt. *~/.popt* Per user configuration file for [**popt**(3)](/popt/3.md). ## BUGS None known. ## AUTHOR Kay Pruefer \\ Udo Stenzel \ ## SEE ALSO [**popt**(3)](/popt/3.md),**fasta**(5)