NCBI BLAST for RIF Web site Altschul, Madden, Schaeffer, Zhang, Miller, Lipman Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaeffer,Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. http://www.pasteur.fr/recherche/unites/RIF/private/ rif rif Blast program perl "blastall -p $value " blastp 1 blastn blastn: nucleotide query / nucleotide db tblastn tblastn: protein query / translated nucleotide db tblastx tblastx: nucleotide query transl. / transl. nucleotide db nb_proc perl " -a 2" 6 perl ! $psi query Sequence File perl " -i $query" 3 8 seqfile perl 1 nucleotid_db perl " -d camlst" 3 perl ($rif =~ /^blastn|^tblastn|^tblastx/) Expect Expect: upper bound on the expected frequency of chance occurrence of a set of HSPs (-e) perl (defined $value && $value != $vdef)? " -e $value":"" 10 5 The statistical significance threshold for reporting matches against database sequences; the default value is 10, such that 10 matches are expected to be found merely by chance, according to the stochastic model of Karlin and Altschul (1990). If the statistical significance ascribed to a match is greater than the EXPECT threshold, the match will not be reported. Lower EXPECT thresholds are more stringent, leading to fewer chance matches being reported. Fractional values are acceptable. filter perl " -F F -T F" 5 txtoutput perl " > rif.txt" 7 htmloutput perl ($_html) && ($view_alignments ne "7") perl " && html4blast -o rif.html -s -g rif.txt" 8 tmp_outfile rif.txt blast_output perl $view_alignments ne "7" htmlfile rif.html