Uses of Interface
org.strbio.mol.lib.Blast

Packages that use Blast

org.strbio.local	These classes are for running or exchanging data with local programs (other programs installed on your computer).
org.strbio.mol	These classes represent objects or concepts useful to structural biologists.
org.strbio.mol.lib	These classes represent conceptual objects used in structural biology algorithms.
org.strbio.net	These classes are for running or exchanging data with non-local programs (i.e., programs that you run by submitting data to a web page).

Uses of Blast in org.strbio.local

Classes in org.strbio.local that implement Blast

class	BlastClient Runs a local copy of blastclient.
class	BlastP Runs a local copy of blastp.
class	BlastPAdapter This is an adapter class for Blast which should extend both Program and BlastAdapter.
class	PSIBlastP Runs a local copy of psiblast.
class	PSIBlastP2 Runs a local copy of psiblast.
class	TBlastN Runs a local copy of tblastn.

Uses of Blast in org.strbio.mol

Methods in org.strbio.mol with parameters of type Blast

void	ProfilePSI.blast(Printf outfile, Blast blastServer) Run BLAST on this profile, using a specified server.
void	ProfileSet.blast(Printf outfile, Blast blastServer) Run BLAST on all proteins in the set, using a specified blast server.
void	Profile.blast(Printf outfile, Blast blastServer) Run BLAST on this profile, using a specified server.

Uses of Blast in org.strbio.mol.lib

Subinterfaces of Blast in org.strbio.mol.lib

interface

PSIBlast Interface for common PSI-blast related routines.

Classes in org.strbio.mol.lib that implement Blast

class

BlastAdapter Adapter class to implement the routines in Blast.

Uses of Blast in org.strbio.net

Classes in org.strbio.net that implement Blast

class	BlastNCBI Does a BlastP search in the NR database at NCBI, using the main web gateway.
class	BlastNCBI2 Does a BlastP search in the NR database at NCBI, using the "stable" web gateway.
class	BlastWeb Does a BlastP search in the NR database at over the web.
class	PSIBlastNCBI Does a PSI-BLAST search in the NR database at NCBI, using the main web gateway.
class	PSIBlastWeb Does a PSI-BLAST search in the NR database over the web.