On Wed, 2004-02-18 at 14:38, Dan Bolser wrote: > Hello, > > I want to quickly find a sequence for a list of sequence id's, so I > thought I would use formatdb to index the fasta format database and then > use the sequence retreival tool to query this index. > > Is formatdb included in the NCBI rpm available from > > http://downloads.scalableinformatics.com/downloads/ncbi/ Yes. The binary RPMs contain compiled executables which install into /usr/local/bin. To run formatdb you would run /usr/local/bin/formatdb > When I try to install this rpm (src), it doesn't show up when I search rpm > -q -a output. > > I am just doing > > rpm -i NCBI-2.2.7-6.src.rpm (returns no error messages) > > Is this correct? Only if you intend to rebuild from source :). If you have a look in the /usr/src/redhat/SOURCES directory, you will see ncbi.tar.gz (the NCBI tools tarball of source). In /usr/src/redhat/SPECS you will see ncbi-toolkit.spec which will happily turn this tarball into a binary RPM, after a long compilation process. It might be simpler to grab http://downloads.scalableinformatics.com/downloads/ncbi/NCBI-2.2.7-6.i686.rpm and use this if you don't need to recompile. Please do let me know if there are any issues with the build. Joe -- Joseph Landman, Ph.D Scalable Informatics LLC email: landman@scalableinformatics.com web: http://scalableinformatics.com phone: +1 734 612 4615