Bioinformatics databases
- 2. TOPICS SEQUENCE MOTIFS DATABASES
- 3. Sequence motif : In genetics, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance. For proteins, a sequence motif is distinguished from a structural motif, a motif formed by the three-dimensional arrangement of amino acids which may not be adjacent.
- 4. There are mainly two types of sequence motif databases such as: P fam Prosite
- 5. Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The most recent version, Pfam 31.0, was released in March 2017 and contains 16,712 families. Uses: The general purpose of the Pfam database is to provide a complete and accurate classification of protein families and domains.
- 6. It is used by experimental biologists researching specific proteins, by structural biologists to identify new targets for structure determination, by computational biologists to organise sequences and by evolutionary biologists tracing the origins of proteins. Pfam has also been used in the creation of other resources such as iPfam, which catalogs domain- domain interactions within and between proteins, based on information in structure databases and mapping of Pfam domains onto these structures
- 7. Features : For each family in Pfam one can: View a description of the family Look at multiple alignments View protein domain architectures Examine species distribution Follow links to other databases View known protein structures
- 9. The Pfam database is licensed under the GNU General Public License, which basically makes it available to anyone. But imposes the restriction that derivative works (new databases, modifications) must be made available in source form.
- 10. PROSITE : (www.expasy.ch/prosite/) PROSITE is a protein database. It consists of entries describing the protein families, domains and functional sites as well as amino acid patterns and profiles in them. PROSITE was created in 1988 by Amos Bairoch, who directed the group for more than 20 years. Since July 2018, the director of PROSITE and Swiss-Prot is Alan Bridge
- 11. PROSITE's uses include identifying possible functions of newly discovered proteins and analysis of known proteins for previously undetermined activity. PROSITE offers tools for protein sequence analysis and motif detection (see sequence motif, PROSITE patterns). It provides additional information about functionally or structurally critical amino acids.