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Interfacing similarity search software with the sequence retrieval system ACNUC.

D G Higgins¹, M Gouy

¹Department of Genetics, Trinity College, Dublin 2, Ireland.

Computer Applications in the Biosciences : CABIOS

|September 1, 1987

Summary

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This study introduces an efficient FORTRAN 77 method for linking sequence similarity search software with the ACNUC system. The approach simplifies database searching using indexing, avoiding slow linear scans.

Area of Science:

Bioinformatics
Computational Biology
Database Management

Background:

Sequence similarity searches are crucial for biological research.
Existing methods for interfacing search software with retrieval systems can be complex.
The ACNUC system is a fast sequence retrieval system.

Purpose of the Study:

To describe a straightforward and efficient method for interfacing sequence similarity search software with the ACNUC system.
To reduce the complexity of integrating bioinformatics tools.

Main Methods:

Developed a method using FORTRAN 77.
The interface requires minimal additional code (approx. 12 lines).
Utilized simple indexing techniques for sequence retrieval.

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Main Results:

The described method is easy to implement, requiring no text-processing code.
Achieved efficient sequence retrieval by avoiding linear searches of large database files.
Demonstrated the effectiveness of indexing for fast data access.

Conclusions:

The FORTRAN 77 method provides an efficient and simple solution for integrating sequence similarity search tools with ACNUC.
This approach enhances the usability of bioinformatics databases.
Indexing techniques offer a significant performance improvement for sequence retrieval.