GENSCAN 1.0 Gene Identification C. Burge Burge, C., Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78-94. Burge, C., Karlin, S. (1997) Gene structure, exon prediction, and alternative splicing. (in preparation). Burge, C. (1997) Identification of genes in human genomic DNA. PhD thesis, Stanford University, Stanford, CA. Burset, M., Guigo, R. (1996) Evaluation of gene structure prediction programs. Genomics 34, 353-367. nucleic:translation gene finding genscan genscan seqlab genscan perl "genscan" 0 seq DNA Sequence File perl " $value" 2 8 seqfile perl 1 parameter_file Parameter file perl " $value" 1 Arabidopsis.smat HumanIso.smat Maize.smat Currently available parameter files are: HumanIso.smat for human/vertebrate sequences (also Drosophila) Arabidopsis.smat for Arabidopsis thaliana sequences Maize.smat for Zea mays sequences output Output parameters 3 verbose Verbose output (-v) perl ($value)? " -v":"" 0 3 Add some extra explanatory information to the text output. This information may be helpful the first few times you run the program but will soon become tiresome (that's why its optional). cds Print predicted coding sequences (-cds) perl ($value)? " -cds":"" 0 3 subopt Identify suboptimal exons (-subopt) perl ($value)? " -subopt $cutoff":"" 0 3 The default output of the program is the optimal 'parse' of the sequence, i.e. the highest probability gene structure(s) which is present: the exons in this optimal parse are referred to as 'optimal exons' and are always printed out by GENSCAN. Suboptimal exons, on the other hand, are defined as potential exons which have probability above a certian threshold but which are not contained in the optimal parse of the sequence. Suboptimal exons have a variety of potential uses. First, suboptimal exons sometimes correspond to real exons which were missed for whatever reason by the optimal parse of the sequence. Second, regions of a prediction which contain multiple overlapping and/or incompatible optimal and suboptimal exons may in some cases indicate alternatively spliced regions of a gene (Burge & Karlin, in preparation). cutoff Cutoff for suboptimal exons perl "" 3 The cutoff is the probability cutoff used to determine which potential exons qualify as suboptimal exons. This argument should be a number between 0.01 and 0.99. For most applications, a cutoff value of about 0.10 is recommended. Setting the value much lower than 0.10 will often lead to an explosion in the number of suboptimal exons, most of which will probably not be useful. On the other hand, if the value is set much higher than 0.10, then potentially interesting suboptimal exons may be missed. perl $subopt ps Create Postscript output (-ps) perl ($value)? " -ps $psfname $scale" : "" 0 3 scale Scale for PostScript output (bp per line) perl "" 3 perl $ps psfname Filename for PostScript output perl "" genscan.ps 3 perl $ps