Software Listing: Amino Acids

  • ProCoS
  • License: Freeware
  • Price: 0.00
  • Rating

Author: Lavanya Rishishwar

ProCoS (Protein Composition Server, script version) is a one stop shop for computing all the possible types of peptide compositions, whether it be Pseudo Amino Acid Composition (PAAC)(Chou 2001), Amphiphilic Pseudo Amino Acid Compostion (APAAC)(Chou 2005), Five Factor Solution Score (5FSS)(Chou & Cai 2005), Amino Acid Composition, Dipeptide Composition, Tripeptide Composition... Polypeptide Composition. The program was previously released as an applet as well as a server. But complying with open-sourcing the research, we have released the script version as well.

  • Platform: WinOther

At the outset, the goal of this program is to provide a suite of tools to aid in the back-translation of amino acid sequences in a manner that provides useful information for synthetic gene design.
pyBackTranslate License - GNU General Public License version 3.0 (GPLv3).

  • Platform: WinOther

MSF is a Java-based tool to find all possible mutation sites from next generation sequencer data (SNP) with visualization of the region with annotations (chromosome, position, plasmid, gene, amino acid and nucleotide).
MSF Mutation Sites Finder License - GNU General Public License (GPL).

  • Platform: WinOther

PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments, in an automatic way or drive by users.
ProtoGene License - GNU Library or Lesser General Public License (LGPL).

  • Platform: WinOther
  • SPASTv
  • License: Freeware
  • Price: 0.00
  • Rating

SPAST is a PC-based software tool developed for large-scale quantitative assessment of the bias or asymmetry, if any, in substitution patterns of all possible pairs of nucleotide/amino acid residues between groups of orthologs of two or more species.
SPASTv License - Academic Free License (AFL).

  • Platform: WinOther

AMINO STB Video-On-Demand MiddleWare
Flex-Stb-Video License - Apache License V2.0.

  • Platform: WinOther
  • miReader
  • License: Freeware
  • Price: 0.00
  • Rating

miReader is a simple application designed to analyze RNA data and in order to identify ribonucleic acids.

miReader is very easy to use: just browse for the input file, set the destination directory and the number of processors, choose the model and press the 'Run' button. It supports the following models: Homo sapiens, Arabidopsis, Oryza, C. elegans and Drosophila.


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  • Platform: Windows 7, Windows 8, WinOther, WinVista
  • MAFFT
  • License: Shareware
  • Rating

MAFFT was developed as a small, easy-to-use and Command Line-based multiple sequence alignment application.

MAFFT is a software that offers a range of alignment methods for amino acid or nucleotide sequences.


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  • Platform: Win7 x64, Windows 7, Windows 8, WinOther, WinVista

How do strong and weak acids differ? Use lab tools on your computer to find out! Dip the paper or the probe into solution to measure the pH, or put in the electrodes to measure the conductivity.

Then see how concentration and strength affect pH. Can a weak acid solution have the same pH as a strong acid solution?

Acid-Base Solutions is a handy utility designed for those who want to learn about acid solutions.

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  • Platform: Windows 7, WinOther, WinVista

Genomic Peptide Finder is a compact toolbox that can help you match de novo predicted amino acid sequences to the genomic DNA sequence. The gpfindex tool can process fasta DNA files in order to create GPF index files.

The applications can be used in command line mode or by using the Command Prompt window. To start using the program you can read the documentation provided by the developer here.


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  • Platform: WinOther

Some (Dutch) IPTV providers offering an Amino set-top box use dynamic IP assignment. This is not handy for people who use a media center, since the DHCP request/response is specific for the STB/provider. Therefor, it is impossible to use the Windows DHCP client. This project implements a Windows DHCP client for users of an Amino STB..

  • Platform: Win7 x64, Windows 7, WinOther, WinVista

The program uses the free food composition database from the USDA. This free nutritional analysis software was written for Unix systems (I use Linux), but can be compiled on just about any system with a C compiler. (To get a free C compiler, Windows people might look at Cygwin or MinGW, and Mac people might look at xcode.) By experimenting with NUT, you can find the optimal level of the various nutrients and how to implement this with foods available to you. NUT can help reconstruct the lost instruction manual to your care and feeding because, when the authorities and crackpots disagree on the proper human diet, you can design an experiment using the food composition tables to discover the truth!

Features of NUT include:

7636 foods and 146 nutrients--the complete, latest USDA database
Foods easy to find...

  • Platform: WinOther

UVScan is software for the visualization of skin damages caused by UV Exposure.

The human skin undergoes certain changes when exposed to UV light to protect against damage. The skin's uppermost layer thickens, blocking UV light. The pigment-producing skin cells produce increased amounts of melanin, which tans the skin.

Exposure to sunlight prematurely ages the skin. Exposure to ultraviolet light is responsible for the fine and coarse wrinkles; irregular pigmentation; brown and spots; and leathery skin.

The more Sun exposure a person has, the higher the risk of skin cancers.

  • Platform: Win2000, WinOther

CQFZ Magic Problems Creator for Chemistry has a powerful Wizard to help you Create your own custom problems collections - Inorganic nomenclature: Oxides, salts, acids, mono and polyatomic ions, halides,hydroxides - Organic nomenclature: Linear Branched chains, Alkanes, Cycloalkanes, Oxygen and Nitrogen functional groups - Easy and fast to use. - User's manual in PDF format - More info at www.vaxasoftware.com/pc/index.html.

  • Platform: Win2000, WinOther, WinVista

Squint is an advanced alignment tool. It brings together algorithmic alignment of molecular sequences, with human editing. It is an extension of the alignment editor available in Pebble. The easy to use and powerful interface provides the following

features:

Import/export sequence/alignment data in a number of formates (Fasta/Nexus/Clustal/Phylip).
Edit the placement of the gaps in an alignment, with the option of two views of the data being edited (with one view showing the data as DNA, the other as amino acid for example).
Dynamic feedback on the effect of changes to the alignment on one or more measures of alignment score.

  • Platform: WinOther

TREECON is a software package developed primarily for the construction and drawing of phylogenetic trees on the basis of evolutionary distances inferred from nucleic and amino acid sequences. The evolutionary distance is computed for all pairs of organisms (or sequences) and a phylogenetic tree is inferred by considering the relationship between these distance values. In pairwise distance methods, the dissimilarity (fraction of substitutions) is usually converted into evolutionary distance by correcting for multiple mutations. The most frequently used equations to convert dissimilarities into distances are implemented in TREECON.

  • Platform: WinOther

ANTHEPROT 3D is a molecular graphics program intended for the visualisation of proteins, nucleic acids from RCSB archive. The program is aimed at display, teaching and generation of publication quality images.

The 3D module of ANTHEPROT 3D has been completely written in OPENGL for maximal graphic speed. It is now available as a standalone program but can be still associated with the general ANTHEPROT plateform of protein sequence analysis. An image gallery and video are available which demonstrate the software graphic capabilities..

  • Platform: WinOther
  • McRate
  • License: Freeware
  • Price: 0.00
  • Rating

McRate is a program for detecting conserved amino-acid sites by computing the relative evolutionary rate for each site in the multiple sequence alignment (MSA). In contrast to other existing programs McRate considers all possible phylogenetic scenarios among the sequences under study, rather than relying on a single best tree..

  • Platform: WinOther

ForCon is a user-friendly software tool for the conversion of nucleic acid and amino acid sequence alignments. Many software packages for sequence alignment and the construction of evolutionary trees have implemented their own standard of saving and reading sequence alignments. To circumvent the labourious work of manually converting alignment formats with the use of a word processor, this program was written: it converts these formats automatically..

  • Platform: WinOther

The free trail version has no restrictions but contains ads.

Curious about the number of calories, carbohydrates, protein and fatty acids in your food? And also interested in whether the amount fits in your dialy recommended need?

Then FoodBuddyLite is a must have!

FoodBuddyLite features information over more than 2000 products. Not only on the basis of its weight (e.g. per 100 grams) but also on the basis of units like a spoon, cup, the amount used on a slide of bread, etc.

The information used by FoodBuddyLite is originated from the Dutch National Institute for Public Health and the Environment (Ministry of Health, Welfare and Sport).

  • Publisher: VelitNL
  • Date:
  • Size: 2048 KB
  • Platform: Windows Phone, WinMobile

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