Secondary Databases

A biological database is a large, organized body of persistent data, usually associated with computerized software designed to update, query, and retrieve components of the data stored within the system.
The chief objective of the development of a database is to organize data in a set of structured records to enable easy retrieval of information.
Based on their contents, biological databases can be either primary database or secondary databases.
Among the two, secondary databases have become a biologist’s reference library over the past decade or so, providing a wealth of information on just any research or research product that has been investigated by the research community.

Table of Contents

Introduction

Sequence annotation information in the primary database is often minimal.
To turn the raw sequence information into more sophisticated biological knowledge, much post-processing of the sequence information is needed.
This begs the need for secondary databases, which contain computationally processed sequence information derived from the primary databases.
Thus, secondary databases comprise data derived from the results of analyzing primary data.
Secondary databases often draw upon information from numerous sources, including other databases (primary and secondary), controlled vocabularies and the scientific literature.
They are highly curated, often using a complex combination of computational algorithms and manual analysis and interpretation to derive new knowledge from the public record of science.
The amount of computational processing work, however, varies greatly among the secondary databases; some are simple archives of translated sequence data from identified open reading frames in DNA, whereas others provide additional annotation and information related to higher levels of information regarding structure and functions.

Secondary databases contain information derived from primary sequence data which are in the form of regular expressions (patterns), Fingerprints, profiles blocks or Hidden Markov Models.
The type of information stored in each of the secondary databases is different. But in secondary databases, homologous sequences may be gathered together in multiple alignments.
In multiple alignments, there are conserved regions that show little or no variation between the constituent sequences. These conserved regions are called motifs.
Motifs reflect some vital biological role and are crucial to the structure of the function of the protein. This is the importance of the secondary database.
So by concentrating on motifs, we can find out the common conserved regions in the sequences and study the functional and evolutionary details or organisms.

Some of the common secondary databases include:

It was the first secondary database developed.
Protein families usually contain some most conserved motifs which can be encoded to find out various biological functions.
So by using such a database tool, we can easily find out the family of proteins when a new sequence is searched. This is the importance of PROSITE.
Within PROSITE motifs are encoded as a regular expression (called patterns).
Entries are deposited in PROSITE in two distant files. The first file gives the pattern and lists all matches of pattern, whereas the second one gives the details of family, description of the biological role, etc.
The process used to derive patterns involves the construction of multiple alignment and manual inspection.
So PROSITE contains documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.

Most protein families are characterized by several conserved motifs.
All of these motifs can be an aid in constructing the `signatures’ of different families. This principle is highlighted in constructing PRINT database.
Within PRINTS motifs are encoded as unweighted local alignments. So small initial multiple alignments are taken to identify conserved motifs.
Then these regions are searched in the database to find out similarities.
Results are analyzed to find out the sequences which matched all the motifs within the fingerprint.
PROSITE and PRINTS are the only manually annotated secondary databases. The print is a diagnostic collection of protein fingerprints.

The limitations of the above two databases led to the formation of Block database.
In this database, the motifs (here called Blocks) are created automatically by highlighting and detecting the most conserved regions of each family of proteins.
Block databases are fully automated.
Keyword and sequence searching are the two important features of this type of database.
Blocks are ungapped Multiple Sequence Alignment representing conserved protein regions.

Profile database is used to find out the most conserved regions in the sequence alignment. The profile is weighted to indicate modifications (in bioinformatics called INDELS) are allowed in the sequence.
Indels may be the insertion of a new sequence or deletion from the sequence.
Profiles are also known as ‘weight matrices’ to provide a means of detecting distant sequence relationships.

Read Also:

Xiong J. (2006). Essential Bioinformatics. Texas A & M University. Cambridge University Press.
Arthur M Lesk (2014). Introduction to bioinformatics. Oxford University Press. Oxford, United Kingdom
https://www.ebi.ac.uk/training/online/course/bioinformatics-terrified-2018/primary-and-secondary-databases
https://www.omicsonline.org/scholarly/bioinformatics-databases-journals-articles-ppts-list.php
https://www.ncbi.nlm.nih.gov/books/NBK44933/