FastAlert--an automatic search system to alert about new entries in biological sequence databanks.

This paper describes a new tool enabling awareness of new sequence databank entries of interest. The FastAlert system relieves the researcher from the burden of repeating FASTA searches in order to keep up with the rapidly growing amount of information found in biological sequence databanks. The query sequence can be submitted from any computer connected to the Internet.

List update processing (LUP)--solving the sequence database update problem.

Sequence databases of today require frequent updating. Mirror procedures to copy incrementally updated databases as cumulative sets are the preferred method and can be implemented by straightforward scripting. However, limited bandwidth of networks and the increase of data require more powerful paradigms to reduce the workload reliably.

Optimal production of biological documentation: the JAM format.

The current environment for providing documentation for users in molecular biology frequently requires written information for both printed and electronic media. The JAM. (Just Another Metafile) Format requires that only a single file of text is written.

A compression mechanism for sequence databases to improve the efficiency of conventional tools.

This paper describes a method to compress molecular biology databases that are characterized by an increasing proportion of data derived from genome projects. The performance of our tool has been tested on various data files of the EMBL nucleotide sequence database. The best compression ratios were achieved on EST (Expressed Sequence Tags) data, typically derived from large-scale sequence projects.

Sequence databases: an indispensible source for biotechnological research.

The current status of the nucleic acid and protein sequence databases and their importance for the development of a potent biotechnological infrastructure is described. The basic technological background for the data collection and data distribution services are elucidated.