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		WU-Blast 2.0 [Nov-2000] Rapid Sequence Database Search Programs using the BLAST Algorithm FAQ Indexing January 28th 2003 Readme on January 28th 2003 update Readme on November 21th 2001 update Readme on November 09th 2000 update Readme on October 24th 2000 update Note: For compatibility reasons with GCG all blast modules at the University of Zürich start with capilal letters: Blastn, Blastx, Blastp, TBlastx and TBlastn Wu-Blast now offers an emulation of the NCBI blastall programm called wu-blastall. You find special features and information on wu-blastall here. Please take the time to read this documentation! wu-blastall can be invoked from the command line. Just type: > wu-blastall [options] A comprehensible guide to NCBI Blast and Blast in general can be fond at NCBI. Blast runs as a GCG module and as standalone program. The standalone WU-Blast can be run on a maximum of 4 processors whereas GCG Blast uses only one. Nevertheless, PLEASE use a maximum of two processors for longer jobs and a maximum of 3 processors for very short jobs. Blast consists of different modules for DNA and Protein analyses. On the Challenge Blast can search the DNA and Protein non redundant databases (dna and protein) as well as the weekly updates of EMBL, GenBank and Swissprot (dna_new and prot_new). The newest Transcription Factor Database (tfd) can also be searched. Your sequence should be in FASTA format. Under GCG you can convert any GCG sequence to FASTA format with the command > tofasta test.seq. The output sequence will have the extension tfa. Example: > Blastn dna test.tfa Available Blast databases at the Center for Computing services DB-Name DB-Type Description protein Amino Acid NR Protein (SP,PIR,NRL3D,TREMBL) nrl_3 Amino Acid Brookhaven Database trembl Amino Acid TREMBL Database dna Nucleotide NR DNA (EMBL,GB without est) dna_est Nucleotide NR DNA_EST (EMBL,GB) bacteria Nucleotide Bacterial genomic DNA (hinf, mgen, mjan) yeast Nucleotide Yeast Chromosome 1-16 plant Nucleotide NR DNA_PLANT (EMBL fun pl, GB pl1 pl2) Note: The different Blast-commands will only find the databases fitting the respective nucleic acid or amino acid search sequence and search command.