ESTGENOME: a program to align spliced DNA sequences to unspliced genomic DNA

spliced DNA to unspliced genomic DNA. It is written in ANSI C and has been tested under Digital OSF3. 2. The spurce code and documentation are available from ftp: // www. sanger. ac. uky ftp/pub / badger/estgenome. 2. tar. Z. The prediction of genes in uncharacterized genomic DNA sequence is currently one of the main problems facing sequence annotators. Methods based on de novo prediction, e. g. searching for motifs like the splice-site consensus, or on statistical properties such as biased codon usage, etc. (Solovyev et al. , 1994; Hebsgaard et al. , 1996) have been only partially successful, and investigators have often found that the surest way of predicting a gene is by alignment with a homologous protein sequence (Birney et al. , 1996; Gelfand et al. , 1996; Huang and Zhang, 1996), or a spliced gene product an expressed sequence tag (EST), mRNA or cDNA,