The FASTA program is a more sensitive derivative of the FASTP program, which can be used to search protein or DNA sequence data bases and can compare a protein sequence to a DNA sequence data base by translating the DNA data base as it is searched.
They can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity. We have developed three computer programs for comparisons of protein and DNA sequences. The system provides the user with the ability to facilitate and modify the analysis and modeling in real time. This reduces the number of sequences to be searched from N to O ( N) on average, and hence greatly reduces the search time, where N is the number of sequences in the original database. To overcome the computational bottleneck in the database similarity search used in the gene identification process, we have developed an effective way to partition a database into a set of sub-databases of "related" sequences, and reduced the search problem on a large database to a signature identification problem and a search problem on a much smaller sub-database. A graphics-based user interface provides an environment which allows the user to interactively control the evidence to be used in the gene identification process. The core of the system is a multiple-gene structure identification program, which predicts the most "probable" gene structures based on the given evidence, including pattern recognition, EST and protein homology information.
This paper presents a computer system for analyzing and annotating large-scale genomic sequences.
0 kommentar(er)
