Software Listing: Amino Acid Sequence

The Protein Stability program was developed to help you explore and analyze the energy requirements of each amino acid in the protein sequence derived from various applied kinetic and thermodynamic quantities.

The algorithm is strongly dependent both on kinetic quantities such as atomic solvation energies and solvent accessible surface area and thermodynamic quantities viz. enthalpy, entropy, heat capacity, etc.

The hydrophobicity pattern of protein was considered as the important component of protein stabilization.

Protein stability, the most important aspect of molecular dynamics and simulations, requires sophisticated instrumentations of molecular biology to analyze its kinetic and thermodynamic background.

  • Platform: WinOther

GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more. It is free software under GPLv2+. Requested Features: - Import of Vector NTI Database/Data - Export of Map as Vector Graphic - Edit and move around Plasmid Map Layout - Allow storage in database of complete sequencing files (if space is a concern maybe an upper limit of 2 sequences for each clone would suffice) - Add sections in the database to allow record of box storage position of clone's DNA, glycerol stock, primers - Allow closing of files with Ctrl-W - Clicking a region in the vector map should take the cursor to that region in the sequence viewer.

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

ATGC is an application containing a pack of useful algorithms in user-friendly interface for aligning nucleotide sequences, searching consensus and restriction sites, predicting amino acid sequence, docking contigs and so on..

  • 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

This app is a simple simulator of central dogma for biology and bioinformatics.

DNA(Gene) sequence will be converted into mRNA and Amino Acid sequence.

Various codon tables can be selected for translation.

Disclaimer
This app is provided "as is", without warranty of any kind.
Your use of the app is at your own risk.

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  • Publisher: BFrontier
  • Date: 26-02-2015
  • Size: 17 KB
  • Platform: Android 1.x, Android 2.x, Android 3.x, Android 4.4, Android 4.x

Pseudo amino acid composition or PseAAC, is designed as an accessible and Open Source algorithm that could convert a protein sequence into a digital vector that could be processed by pattern recognition algorithms.

The design of PseAAC Builder incorporated the sequence order information to improve the conventional amino acid compositions.

The application of pseudo amino acid composition is very common, including almost every branch of computational proteomics.

You can now use the cross-platform PseAAC-Builder tool for generating protein pseudo-amino acid compositions.

  • Platform: WinOther
  • 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

Multifunctional Biochemistry Software Package Integrated With: Amino Acid Analysis, Building Block Composition, Digestion, Elemental Analysis, Fragmentation, Isotopic Distribution, Combinatorial Library, Molecular Weight, Motif, and Helix Wheel/Net..

  • Platform: Win2000, Win7 x32, Win7 x64, WinOther, WinVista, WinVista x64

Ever got confused while remembering all the various physical properties of all the standard 20 amino acids? Then use Amino Acid Finder!! It has a built-in database and contains information about all the physical properties and lets you to search them.

  • Platform: Linux, Mac OS X, WinOther

PutGaps is a simple command line utility designed to insert gaps into DNA alignment files by using the amino acid equivalent. The program can be used for conserving codon positions into aligned nucleotide and amino acid files.

You can use the program in the console in order to view the available commands and enter the operation arguments.


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  • Platform: WinOther

Having trouble remembering the one letter, three letter amino acid names? How about the polarity? Use this App as a quick reference to learn..

  • Platform: Android 4.x

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
  • BiasViz
  • License: Freeware
  • Price: 0.00
  • Rating

BiasViz is a Java applet for visualization of amino acid bias in multiple sequence alignments..

  • Platform: Linux, Mac OS X, WinOther

Basic implementation of K-nearest neighbour Algorithm and the application of KNN to classify protein sequences as transmembrane beta barrel or non-transmembrane beta barrel on the basis of whole sequence amino acid composition given as input..

  • Platform: Linux

A Mass Spectrometer B and Y ion labeling software for proteomics researchers. Peptide sequences can be read from a library and b and y ions will be calculated and sequence can be manipulated by the user (chem. mod. or amino acid mod.).

  • Platform: Linux, Mac OS X, 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

Program allows to convert protein sequence from different formats (as Fasta, PDB, Swiss-protein, Swiss-DNA) to another ones (as Fasta, Swiss-protein and Pure amino acid sequence). You should not think about input format at all. You can simply select all input files and program can recognize automatically in one step each file that contains amino acid sequence. Then you can export some or all sequences to the requested format also in one step.. ProteinSystems - software for research in molecular biology. ProteinSystems - software for research in molecular biology.

  • Platform: Win2000, WinOther

A tool to acquire the amino acid sequences of the essential genes available at the database of essential genes at DEG (http://tubic.tju.edu.cn/deg/) and convert it to fasta sequence.
OpenDEGParser License - GNU General Public License (GPL).

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

Simprot allows for several models of amino acid substitution (PAM, JTT
and PMB), allows for gamma distributed sites rates according to Yang's model, and implements a
parameterised Qian and Goldstein distribution model for insertion and deletion..

  • Platform: WinOther

Toolkit to examine the topology of a phylogenetic tree, place amino acid substitutions on specific branches, polarize them and compare amino acid sequences of homologous proteins to answer a wide range of questions about protein evolution..

  • Platform: Linux, Mac OS X, WinOther

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