GRAILCLNT 1.3b Grail client Xu, Einstein, Mural, Shah, Uberbacher Xu, Y., Einstein, J. R., Mural, R.J., Shah, M. and Uberbacher, E.C., (1994) An Improved System for Exon Recognition and Gene Modeling in Human DNA Sequences, Published Presentation: The Second International Conference on Intelligent Systems for Molecular Biology, Stanford University, San Francisco, CA, August 14-17, 1994. nucleic:translation gene finding grailclnt grailclnt perl "cat grail_input_* > grail_input; grailclnt -host grailsrv.lsd.ornl.gov -port 2050 < grail_input " 2 seq Sequence perl " ln -s $seq grail_input_a4 ;" 1 13 feature Which feature? perl ($value eq "cpg" || $value eq "rpttv" || $value eq "smprpt")? "\\n\\[Request\\_$value\\_1.3\\]\\n\\n" : "\\n\\[Request\\_$value\\_$organism\\_1.3\\]\\n\\n" grail2exons 2 grail1exons grail1aexons grail2exons gap2 polya polIIprom cpg rpttv smprpt fserr The coding recognition portion of the system uses a neural network which combines a series of coding prediction algorithms. There are three basic versions of this neural network, GRAIL 1, GRAIL 1a and GRAIL 2: GRAIL 1 has been in place for about five years. It uses a neural network described in PNAS 88, 11261-11265, which recognizes coding potential within a fixed size (100 base) window. It evaluates coding potential without looking for additional features (information such as splice junctions, etc). GRAIL 1a is an updated version of GRAIL 1. It uses a fixed-length window to locate the potential coding regions and then evaluates a number of discrete candidates of different lengths around each potential coding region, using information from the two 60-base regions adjacent to that coding region, to find the 'best' boundaries for that coding region. GRAIL 2 uses variable-length windows tailored to each potential exon candidate, defined as an open reading frame bounded by a pair of start/donor, acceptor/donor or acceptor/stop sites. This scheme facilitates the use of more genomic context information (splice junctions, translation starts, non-coding scores of 60-base regions on either side of a putative exon) in the exon recognition process. GRAIL 2 is therefore not appropriate for sequences without genomic context (when the regions adjacent to an exon are not present). CpG is available only for Human or Mouse perl $feature eq "cpg" && (! ($organism eq "human" || $organism eq "mouse")) polIIprom is available only for Human or Mouse perl $feature eq "polIIprom" && (! ($organism eq "human" || $organism eq "mouse")) Grail 1 or 1.a is not available for arabidopsis perl $organism eq "arabd" && ($feature =~ /grail1/) fserr is available only for Human or Mouse perl $feature eq "fserr" && (! ($organism eq "human" || $organism eq "mouse")) Grail 1 or 1.a is not available for drosophila perl $organism eq "droso" && ($feature =~ /grail1/) Repetitive DNA is available only for Human or Mouse perl $feature eq "rpttv" && (! ($organism eq "human" || $organism eq "mouse")) polya is available only for Human or Mouse perl $feature eq "polya" && (! ($organism eq "human" || $organism eq "mouse")) E. coli is available only for grail1 or simple repeats perl $organism eq "ecoli" && (! ($feature eq "grail1" || $feature eq "smprpt")) grail_input_a1 organism Organism perl "" human 2 human mouse arabd droso ecoli header Header perl ($value)? "[Option= header]\\n" : "" 0 3 grail_input_a1 exons_options Exons options perl $feature =~ /grail/ translation Translation perl ($value)? "[Option= translation]\\n" : "" 0 3 perl $feature =~ /grail/ grail_input_a1 strandscores Strandscores (grail1) perl ($value)? "[Option= strandscores]\\n" : "" 0 3 perl $feature =~ /grail/ && $feature eq "grail1exons" grail_input_a1 shadowexons Shadowexons (grail 1.a or grail2) perl ($value)? "[Option= shadowexons]\\n" : "" 1 3 This feature is needed for a further polIIpromoters analysis. perl $feature =~ /grail/ && $feature ne "grail1exons" grail_input_a1 clusters Clusters (grail 2) perl ($value)? "[Option= clusters]\\n" : "" 1 3 This feature is needed for a further Gene Modelling analysis with GAP2 or polIIpromoters. perl $feature =~ /grail/ && $feature eq "grail2exons" grail_input_a1 gap_options Gene modelling options perl $feature eq "gap2" cluster_file grail2exons results file perl ($value)? "sed -n \\"/^.Start clusters/,/^.End clusters/p\\" $cluster_file > grail_input_b4 ;" : "" 1 For gap2 (gene assembly) the cluster tables returned by grail2exons must be included. So what you have to do here is to put your grail2exons results, the program will extract clusters from this data. perl $feature eq "gap2" grail_cluster perl 1 modelexon_translation Gene model exons translation perl ($value)? "[Option= modelexon_translation]\\n" : "" 0 3 perl $feature eq "gap2" grail_input_a1 genemodel_translation Entire gene models translation perl ($value)? "[Option= genemodel_translation]\\n" : "" 0 3 perl $feature eq "gap2" grail_input_a1 auto_strand AUTO STRAND perl ($value)? "[Params= AUTO_STRAND $start_strand $end_strand]\\n" : "" 1 4 perl $feature eq "gap2" grail_input_a1 start_strand AUTO STRAND start perl "" perl $feature eq "gap2" && $auto_strand grail_input_a1 end_strand AUTO STRAND end perl "" perl $feature eq "gap2" && $auto_strand grail_input_a1 forward_strand FORWARD_STRAND perl ($value)? "[Params= FORWARD_STRAND]\\n" : "" 0 4 perl $feature eq "gap2" && ! $auto_strand grail_input_a1 reverse_strand REVERSE_STRAND perl ($value)? "[Params= REVERSE_STRAND]\\n" : "" 0 4 perl $feature eq "gap2" && ! $auto_strand grail_input_a1 polIIprom_options Pol II Promoters options perl $feature eq "polIIprom" grail2_file grail2exons results file perl ($value)? " ln -s $grail2_file grail_input_b2 ;" : "" 1 For Pol II promoters, all the results of grail2 must be included. The [Start/end header] lines must be removed. perl $feature eq "polIIprom" grail_cluster perl 1 fserr_options fserr options perl $feature eq "fserr" fserr_strand Strand perl "[Params= $value]\\n" AUTO_STRAND 4 AUTO_STRAND FORWARD_STRAND REVERSE_STRAND perl $feature eq "fserr" grail_input_a1 rpttv_organism perl "\\n\\n[Params= $organism]\\n\\n" 4 perl $feature eq "rpttv" grail_input_a1 start_seq perl "\\n\\n[Start DNASequence]\\n\\n" grail_input_a3 end_seq perl "\\n\\n[End DNASequence]\\n\\n" grail_input_a5 end_request perl "\\n\\n[End_Request]\\n\\n" grail_input_z9 input_file grail_input outfile Result file perl ($value)? " > $value" : "" grailclnt.txt 10 grail_cluster perl $feature eq "grail2exons"