PSORT
Encyclopedia
PSORT is a bioinformatics
tool used for the prediction of protein localisation sites in cell
s. It receives the information
of an amino acid
sequence and its species of origin, e.g. Gram-negative bacteria
as inputs. Then it analyses the input sequence by applying the stored rules for various sequence features of known protein sorting signals. Finally, it reports the possibility for the input protein to be localised at each candidate site with additional information.
Researchers using this tool can predict with some degree of reason, where in a cell a protein is most likely to localise to. This is because proteins are localised by cell machinery that recognises signal peptide
sequences (similar to a postal address) and moves the protein the appropriate location. The signal peptide is often cleaved off after the destination is reached. PSORT uses known signal peptide sequences to analyse and predict what an input sequence is most likely to cause a localisation to.
Protein localisation is important because it supports a proposed role that a protein may have. For instance, catalase enzymes (proteins that convert peroxide into water and oxygen) should be expected to localise to a peroxisome because that is an area of high peroxide activity. By analysing a signal peptide sequence and visual localisation by GFP
expression, strong evidence is obtained for this role.
The program was written by Dr Kenta Nakai from the Human Genome Center at the Institute for Medical Science, University of Tokyo
, Japan and is available free for all users.
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
tool used for the prediction of protein localisation sites in cell
Cell (biology)
The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos....
s. It receives the information
Information
Information in its most restricted technical sense is a message or collection of messages that consists of an ordered sequence of symbols, or it is the meaning that can be interpreted from such a message or collection of messages. Information can be recorded or transmitted. It can be recorded as...
of an amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
sequence and its species of origin, e.g. Gram-negative bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
as inputs. Then it analyses the input sequence by applying the stored rules for various sequence features of known protein sorting signals. Finally, it reports the possibility for the input protein to be localised at each candidate site with additional information.
Researchers using this tool can predict with some degree of reason, where in a cell a protein is most likely to localise to. This is because proteins are localised by cell machinery that recognises signal peptide
Signal peptide
A signal peptide is a short peptide chain that directs the transport of a protein.Signal peptides may also be called targeting signals, signal sequences, transit peptides, or localization signals....
sequences (similar to a postal address) and moves the protein the appropriate location. The signal peptide is often cleaved off after the destination is reached. PSORT uses known signal peptide sequences to analyse and predict what an input sequence is most likely to cause a localisation to.
Protein localisation is important because it supports a proposed role that a protein may have. For instance, catalase enzymes (proteins that convert peroxide into water and oxygen) should be expected to localise to a peroxisome because that is an area of high peroxide activity. By analysing a signal peptide sequence and visual localisation by GFP
Green fluorescent protein
The green fluorescent protein is a protein composed of 238 amino acid residues that exhibits bright green fluorescence when exposed to blue light. Although many other marine organisms have similar green fluorescent proteins, GFP traditionally refers to the protein first isolated from the...
expression, strong evidence is obtained for this role.
The program was written by Dr Kenta Nakai from the Human Genome Center at the Institute for Medical Science, University of Tokyo
University of Tokyo
, abbreviated as , is a major research university located in Tokyo, Japan. The University has 10 faculties with a total of around 30,000 students, 2,100 of whom are foreign. Its five campuses are in Hongō, Komaba, Kashiwa, Shirokane and Nakano. It is considered to be the most prestigious university...
, Japan and is available free for all users.