bblast provides an easy way to query protein and nucleotide local or remote databases (through the network or email servers at NCBI) using any of the blast programs and all their supported options.
bblast permits one or many sequences to be searched against one or many databases using several different BLAST programs. bblast eliminates the tedious task of manually querying the server for each individual sequence and presents a user-friendly interface to searching databases using the blast programs.
Presently bblast supports the following blast (v 1.4) programs:
blastn blastp blastx tblastn tblastxfor searches against all the databases currently maintained at NCBI, as well as any local databases.
bblast is an ideal way to perform batch database searches or regular queries to molecular sequence databases; it can be used interactively (where the user sets various query parameters) or in batch mode (where parameters are supplied using command-line switches, options and arguments).
bblast shields the infrequent or non-power user from many of the complexities of performing blast searches. Where are the databases? What databases can I search? What parameters should I use? How do I get the results back? What if I also have local blast databases to search? What if I have a DNA sequence but want to compare it to a protein sequence database?
In interactive mode, bblast asks the user a series of simple questions so that the desired sequence(s) can be effortlessly searched against the appropriate database(s) with the results returned in the way that best suits the user. bblast detects the type of sequence used for the query (nucleotide or protein), asks (for nucleotide) what the _information_ content of both the query sequence and the database are (i.e. the nucleotide or protein information in a nucleotide sequence). In this way the user is shielded from having to deal with the complexities of all the various blast programs.
In batch mode, bblast can be configured to search databases at the users' convenience (using deliberately scheduled jobs). For instance you may want to query the nucleotide daily update databases at NCBI using tblastx as well as the protein databases using blastp. This is particularly useful when daily searches are required (e.g. when you have a sequence but it does not match anything in the database, you want to check every day to see if something new has been sequenced that matches your sequence).
bblast processes the input file by first extracting each sequence, and determining which datasource (local/remote), database (local, or any of those at NCBI) and method (local, network, email) should be used for the search.
When the user requests a local or network method, the results are saved in files in a local directory specified by the user. If the user performs a request by email, the results are sent back to the user as mail messages by the NCBI server. Either type of results can then be browsed, and sequences in the databases retrieved, using the tbob program (also available from the OGMP).
bblast also can use one or many resource files that permit the user to painlessly configure all possible options to the various blast programs.
This software was written by Pierre Rioux under the supervision of Tim Littlejohn. The development of clever was supported by a grant from the Canadian Genome Analysis and Technology Program (now defunct).