mysql

1. Save all sequences in one flatfile format (NOT MacVector format), e.g. genbank format.
2. Copy all sequences to a Linux/UNIX computer and convert them from Mac format to UNIX format: mac2unix *.gb
3. Write all sequence fiule names into one file: ls *.gb > oligo.lst
4. Convert all sequences into one file of concatenated fasta entries using EMBOSS: seqret -sequence @oligo.lst -osformat fasta. Call the output file "mcbl_oligo_db"
5. Put this fasta file into the blast web servers database directory (.../blast/db)

We updated my server from SuSE 9.3 to 10.1. php5 is the default on 10.1 and my blog software broke. As my blog software is not anymore maintained, I had to switch to another and I selected PluggedOut. The mysql database structures were quite different and this is what I did to do the conversion:

First I dumped the old database into textfiles:

mysqldump -u root -p --tab=/home/jeltsch/temp --fields-terminated-by=| --lines-terminated-by=# journal

There are different possibilities. If you have access to the machine where mysql is running, you should use:
mysqlhotcopy On our RedHat 8 server you just type:
/usr/bin/mysqlhotcopy --user=root --password=sdjksjd journal /path/to/backup/directory Alternatively:
/usr/local/mysql/bin/mysqldump --user=username -p phpgedview >phpgedview The path of the command is specific for the mysql install on a MacOS X machine.