PHYSICO2

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PHYSICO2

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Download this app named PHYSICO2.

Program: 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 Tools, Version 2 .
Version:--v2.0 - improved version of PHYSICO: Gupta et al Bioinformation, 10(2), 105-107, 2014
Author:c)--Shyamashree Banerjee1+, Parth Sarthi Sen Gupta1+, Arnab Nayek1+, Sunit Das1, Vishma Pratap Sur1, Pratyay Seth1, Rifat Nawaz Ul Islam1, & Amal K Bandyopadhyay1*
(1Department of Biotechnology, The University of Burdwan India)
(+Authors equally contribute)

Features

• PHYSICO2 (version 2.0) – It is improved version of our earlier program (PHYSICO: Gupta et al Bioinformation, 10(2), 105-107, 2014) and an automated standalone, multipurpose procedure for analysis of protein se-quences in FASTA format. The program works from UNIX like environment including CYGWIN1 and is interpreted by AWK programming language. It can works on various forms of FASTA files (Input). Based on the form of FASTA-input, relevant outputs are produced. The program is designed such that large database of sequences can be ana-lyzed in a single run. Overall it provides countable advantages over the existing web-tools.
• In a nutshell:
• 1) It works on any form of FASTA format file (RAW or BLOCK, multiline or single lined) with any number of sequences in it.
• 2) Input parameters can either be set as default or user chosen.
• 3) Program also includes AUTOMATED BLOCK FASTA PREPARATION (ABFP) – an extension that allows user to prepare sequence BLOCK FASTA file which is otherwise cumbersome to prepare by manual effort.
• 4) Multi items outputs on: • Composition and class-composition for sequences and for positions (for BLOCK FASTA only) • Positional variability by Shannon, Simpson and Wu Kabat methods. • Positional substitution (contains information on invariant line, conservative and non conservative substitutions) along with mention of conserved position (variability ≤ Shannon threshold) • Positional distribution of first two most diverse (in BLOCK) and highest con-served residues. • pI and pI profile using six different pI scales. • Extinction co-efficient, Aliphatic Index, GRAVY, Molecular weight and mean molecular weight for all sequences present in FASTA file. Results are ar-ranged in systematic manner in excel column. Apart from these, GRAND AV-ERAGES for 46 other properties are computed for all sequences. • Window dependent analyses for 46 different properties.

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