Tag: Amino Acid

AIS – Classify Amino Acids

AIS

:: DESCRIPTION

AIS (Almost Invariant Sets) is a program which uses a novel criterion and method to classify amino acids. The goal is to identify sets of amino acids with a high probability of change between elements of the set but small probability of change between different sets by using amino acid replacement matrices and their eigenvectors. After identification of the subsets the quality of the partition is assessed with a conductance measure

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 AIS

:: MORE INFORMATION

Citation:

Kosiol et al. (2004),
A new criterion and method for amino acid classification
Journal of Theoretical Biology 228:97-106.

TreeSAAP 3.2 – Selection of Amino Acid Properties using Phylogenetic Trees model

TreeSAAP 3.2

:: DESCRIPTION

TreeSAAP (Selection of Amino Acid Properties Based on Phylogenetic Trees) measures the selective influences on 31 structural and biochemical amino acid properties during phylogenesis (the history of genealogical development) and performs goodness-of-fit and categorical statistical tests.

::DEVELOPER

McClellan, David

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux

:: DOWNLOAD

TreeSAAP

:: MORE INFORMATION

Citation

TreeSAAP: selection on amino acid properties using phylogenetic trees.
Woolley S, Johnson J, Smith MJ, Crandall KA, McClellan DA.
Bioinformatics. 2003 Mar 22;19(5):671-2

FastMG 20140909 – Estimate Amino Acid Substitution Matrices for large data sets

FastMG 20140909

:: DESCRIPTION

FastMG is simple, fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets

::DEVELOPER

The Computational Biology Institute (IBC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 FastMG

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Oct 24;15:341. doi: 10.1186/1471-2105-15-341.
FastMG: a simple, fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets.
Dang CC, Le VS, Gascuel O, Hazes B, Le QS

MutPred2 – Predicting whether an Amino Acid Substitution in a protein is Deleterious or Neutral

MutPred2

:: DESCRIPTION

MutPred is a web application tool developed to classify an amino acid substitution as disease-associated or neutral in human. In addition, it predicts molecular cause of disease.

::DEVELOPER

MutPred team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MutPred2

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Nov 1;25(21):2744-50. doi: 10.1093/bioinformatics/btp528. Epub 2009 Sep 3.
Automated inference of molecular mechanisms of disease from amino acid substitutions.
Li B, Krishnan VG, Mort ME, Xin F, Kamati KK, Cooper DN, Mooney SD, Radivojac P.

NIAS-Server 1.0 – Neighbors Influence of Amino acids and Secondary Structures in Proteins

NIAS-Server 1.0

:: DESCRIPTION

NIAS is a server to help the analysis of the conformational preferences of amino acid residues in proteins.

::DEVELOPER

SBCB – Structural Bioinformatics and Computational Biology Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Borguesan, B.; Inostroza-Ponta, M.; Dorn, M.
NIAS-Server: Neighbors Influence of Amino acids and Secondary Structures in Proteins.
Journal of Computational Biology. March 2017, 24(3): 255-265.

NAP – Nucleotide Amino Acid Alignment

NAP

:: DESCRIPTION

NAP (Nucleotide Amino Acid Alignment) is a Java interface to the nap C program. The NAP program computes an optimal global alignment of a DNA sequence and a protein sequence without penalizing terminal gaps. NAP handles frameshifts and long introns in the DNA sequence. It delivers the alignment in linear space, so long sequences can be aligned. The experimental results demonstrate that NAP is a sensitive and powerful tool for finding genes by DNA-protein sequence homology.

::DEVELOPER

the Upton lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

NAP

:: MORE INFORMATION

Citation:

Huang X, Zhang J.
Methods for comparing a DNA sequence with a protein sequence.
Comput Appl Biosci. 1996 Dec;12(6):497-506.

Dependency 2.1 – Detect Functional Interactions between Amino Acids in Proteins

Dependency 2.1

:: DESCRIPTION

Dependency is a program using Multiple Interdependency to detect functional interactions between amino acids in proteins.

::DEVELOPER

The Tillier Group

:: SCREENSHOTS

Dependency

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 Dependency

:: MORE INFORMATION

Citation:

Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments
Elisabeth R. M. Tillier and Thomas W. H. Lui,
Bioinformatics (2003) 19: 750-755

ADAPTSITE 1.6 – Detect Natural Selection at Single Amino Acid Sites

ADAPTSITE 1.6

:: DESCRIPTION

ADAPTSITE is a method of detecting positive and negative selection at single codon sites.

::DEVELOPER

Yoshiyuki Suzuki

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOSX
  • C Compiler

:: DOWNLOAD

 ADAPTSITE

:: MORE INFORMATION

Citation:

Suzuki Y. and Gojobori T. (1999)
A method for detecting positive selection at single amino acid sites.
Mol. Biol. Evol. 16:1315-1328.

Amino Acid Tutor 1.1 – Learn Amino Acid Structures and Codes in iPhone

Amino Acid Tutor 1.1

:: DESCRIPTION

Amino Acid Tutor is a great tool to learn amino acid structures and codes (single letter abbreviations). You will get different types of questions, so the learning process will not be boring.

::DEVELOPER

iVanya

:: SCREENSHOTS

aatutor

:: REQUIREMENTS

  • iPhone / iPad

:: DOWNLOAD

  Amino Acid Tutor

:: MORE INFORMATION

GeneticCode 1.4 / GeneticCodePro 1.4 – Genetic Code of Amino Acids

GeneticCode 1.4 / GeneticCodePro 1.4

:: DESCRIPTION

GeneticCode visualizes standard genetic code as well as provides information about 20 amino acids and their abbreviations.

The GeneticCodePro also includes the following functionality:* Amino acid table with the list of all 20 amino acid (in case you need information about a particular amino acid)* Genetic Code Translator that allowes you to translate direct DNA strand to complementary DNA => RNA => protein (in 3 and 1 letter abbreviations)* Codon Table cells are clickable, so it is possible to get amino acid details directly from the Codon Table

::DEVELOPER

iVanya

:: SCREENSHOTS

GeneticCodeP

:: REQUIREMENTS

  • iPhone / iPad

:: DOWNLOAD

 GeneticCode / GeneticCodePro

:: MORE INFORMATION