PHYSICO2: an UNIX based standalone procedure for computation of physicochemical, window-dependent and substitution based evolutionary properties of protein sequences along with automated block preparation tool, version 2

Abstract

Automated genome sequencing procedure is enriching the sequence database very fast. To achieve a balance between the entry of sequences in the database and their analyses, efficient software is required. In this end PHYSICO2, compare to earlier PHYSICO and other public domain tools, is most efficient in that it i] extracts physicochemical, window-dependent and homologousposition-based-substitution (PWS) properties including positional and BLOCK-specific diversity and conservation, ii] provides users with optional-flexibility in setting relevant input-parameters, iii] helps users to prepare BLOCK-FASTA-file by the use of Automated Block Preparation Tool of the program, iv] performs fast, accurate and user-friendly analyses and v] redirects itemized outputs in excel format along with detailed methodology. The program package contains documentation describing application of methods. Overall the program acts as efficient PWS-analyzer and finds application in sequence-bioinformatics.AvailabilityPHYSICO2: is freely available at http://sourceforge.net/projects/physico2/ along with its documentation at https://sourceforge.net/projects/physico2/files/Documentation.pdf/download for all users.

PROPAB: Computation of Propensities and Other Properties from Segments of 3D structure of Proteins

“…The program requires crystallographic structure files as inputs in its working directory as earlier [ 7 , 8 ]. It can process any number of structure files with any number of chains in them.…”

“…Program is written in AWK programming language, which can preferably run in any C shell UNIX prompt including CYGWIN 32 bit and also be made work in B shell LINUX and WINDOWS environment. Presently we are actively engaged in developing web interface to integrate SBION2 and ADSBET2 [ 9 , 10 ] along with other related software tools of our laboratory [ 6 , 7 , 8 , 11 ] such that their availability could reach to all academic users within an integrated web service.…”

“…An efficient procedure would be useful that not only computes and classify amino acid propensities in error-free, user-friendly manner for any number of structures with any number of chains in them but also critically analyzes physicochemical properties of segments of helices, strands and coils by their self-extraction from structure files. Additionally these FASTA files could further be used for the analysis of variability, evolutionary properties [ 6 ], physicochemical and sequence properties [ 7 , 8 ]. It is with this broad perspective in mind; we have developed PROPAB that not only implements the famous Chou and Fasman [ 2 ] method for propensity but also for the extraction of other above mentioned properties.…”

Comparative physicochemical and evolutionary study of SARS-CoV-2 and SARS with special reference to salt bridge and their microenvironment: A plausible explanation for divergency, stability and severity of SARS-CoV-2

“…Block of sequence was prepared by BLOCK by using ABPT [25]. Non-block and block both format were analyzed by PHYSICO2 [26] for calculation of physicochemical properties like amino acid composition, GRAVY, Zimmerman bulkiness, Grantham polarity, aliphatic index etc. The program works from UNIX like environment [27] including CYGWIN1 and is interpreted by AWK programming language [28].…”

POWAINDv1.0: A Program for Protein-Water Interactions Determination

“…3E9l has been analyzed using PHYSICO2 5,6 and Cosurim 7,8 to understand the sequence and structure properties of the protein (Table 1). Following points are noteworthy.…”