PHYSICO: An UNIX based Standalone Procedure for Computation of Individual and Group Properties of Protein Sequences

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Title	PHYSICO: An UNIX based Standalone Procedure for Computation of Individual and Group Properties of Protein Sequences
Authors	Parth Sarthi Sen Gupta¹, Shyamashree Banerjee¹, Rifat Nawaz Ul Islam¹, Sudipta Mondal¹, Buddhadev Mondal² & Amal K Bandyopadhyay¹*
Affiliation	¹Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India; ²Department of Zoology, Burdwan Raj College, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
Email	akbanerjee@biotech.buruniv.ac.in; *Corresponding authors
Article Type	Software
Date	Received January 20, 2014; Accepted January 26, 2014; Published February 19, 2014
Abstract	In the genomic and proteomic era, efficient and automated analyses of sequence properties of protein have become an important task in bioinformatics. There are general public licensed (GPL) software tools to perform a part of the job. However, computations of mean properties of large number of orthologous sequences are not possible from the above mentioned GPL sets. Further, there is no GPL software or server which can calculate window dependent sequence properties for a large number of sequences in a single run. With a view to overcome above limitations, we have developed a standalone procedure i.e. PHYSICO, which performs various stages of computation in a single run based on the type of input provided either in RAW-FASTA or BLOCK-FASTA format and makes excel output for: a) Composition, Class composition, Mean molecular weight, Isoelectic point, Aliphatic index and GRAVY, b) column based compositions, variability and difference matrix, c) 25 kinds of window dependent sequence properties. The program is fast, efficient, error free and user friendly. Calculation of mean and standard deviation of homologous sequences sets, for comparison purpose when relevant, is another attribute of the program; a property seldom seen in existing GPL softwares.
Availability	PHYSICO is freely available for non-commercial/academic user in formal request to the corresponding author (akbanerjee@biotech.buruniv.ac.in).
Keywords	UNIX; physicochemical properties; FASTA; software; protein sequence.
Citation	Gupta et al. Bioinformation 10(02): 105-107 (2014)
Edited by	P Kangueane
ISSN	0973-2063
Publisher	Biomedical Informatics
License	This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.