REPFIN15.TXT REPFIND is a DOS-based computer program that accepts a DNA sequence as input in one of several formats, and produces as output the same sequence in GenBank format with a feature table added to annotate the location and identity of common repeat elements. As a default the program identifies known human repeat elements, but it can be user- extended to identify any sequence of interest to the researcher. Several options allow control of the output, including a feature that replaces all repeat nucleotides with the letter “x” to facilitate database searches. The program may also be modified to identify and exclude vector sequence. The program package comes in three possible formats: 1. As a ZIP file (REPFIN15.ZIP) that can be extracted using the shareware program PKUNZIP or an alternate. 2. As a self-extracting ZIP file (REPFIN15.EXE, or 3. As a UU-Encoded form of one of the above forms (REPFIN15.UAA to REPFIN15.UAF). This can be sent by regular e-mail in a non-binary manner. First make a directory, as follows: cd \ mkdir repfind Copy the compressed file to the \repfind directory. If the file extension ends in UAA to UAF, use the UUD program (available from ftp://ftp.embl-heidelberg.de/pub/software/dos or from ftp://ftp.bchs.uh.edu/gene-server/dos) to convert it to a binary format. If the file extension ends in EXE, simply run it with a -d option to preserve the subdirectory structure. If the file extension ends in ZIP, run PKUNZIP, again using the -d option. The following files are extracted: \repfind\repfind.exe - the DOS executable file \repfind\repfind.doc - the manual in Word for Windows 6.0 format. \repfind\repfind.txt - the manual in text format \repfind\human\.REP - human repeat files and P1 vector files \repfind\human\repfind.CFG - configuration files From here follow the instructions in the manual. Note that REPFIND is a free program, and as such is provided without warranty of any kind. I am willing to fix any obvious bugs in the program as time allows. If you find a bug, please notify me at the e-mail address below. Gordon B. Hutchinson October, 1995 hutch@NetShop.bc.ca