first previous next last contents



find_renz -- Identifies the position of a cut site within a sequence


find_renz [-vp] enzyme filename ...


find_renz may be used to determine the position that an enzyme cuts a sequence. It's use as a command line utility is primarily designed for internal use within pregap4 and as a user utility for producing vector-primer files for use with vector_clip. As such it is dedicated to finding one and only one such cut site and considers no cuts sites or multiple cut sites to be an error.

Only one enzyme may be specified, which is given by the enzyme name (upper or lower case is not important). One or more filenames may be specified. If an enzyme does not cut a sequence the message "Enzyme not found in sequence" will be sent to stderr. If an enzyme cuts a sequence more than once the message "Found more than one match" will be sent to stderr. Otherwise output is produced to stdout. This means that wildcards may be used (find_renz -vp smai *.seq >> vpfile) with the output redirected without needing to consider whether the enzyme is suitable for all files matching the wildcard pattern.


Specifies that the output should be in a format suitable for saving to a vector-primer file (to use with vector_clip). Without this only the cut site position is listed.


See section vector_clip(1).

first previous next last contents
This page is maintained by staden-package. Last generated on 22 October 2002.