MargFreq 1.02 – Calculate Marginal Frequencies at each Position of a Nucleotide/Amino Acid Sequence

MargFreq 1.02

:: DESCRIPTION

MargFreq is a relatively user-friendly Windows program that does a repetitive task – calculating the marginal frequencies at each position of a nucleotide/amino acid sequence. This program accepts sequence alignments in many different formats. It also does some rudimentary analysis for covariation.

::DEVELOPER

Stuart Ray, M.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

MargFreq

:: MORE INFORMATION

Before you download software you need to read disclaimer.

 

SBAL 1.8 – Structure-based Amino Acid Sequence Alignments

SBAL 1.8

:: DESCRIPTION

SBAL is intended for multiple protein sequence alignments guided by secondary structure elements. The program provides automatic and semi-automatic alignment features, and also possesses manual editing capabilities.

::DEVELOPER

Hofmann Laboratory, Eskitis Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 SBAL

 :: MORE INFORMATION

Citation

Wang, C.K., Broder, U., Weeratunga, S.K., Gasser, R.B., Loukas, A., Hofmann, A. (2012)
SBAL: a practical tool to generate and edit structure-based amino acid sequence alignments.
Bioinformatics 28, 1026-1027.

PLAAC – Prion-Like Amino Acid Composition

PLAAC

:: DESCRIPTION

PLAAC searches protein sequences to identify candidate prion subsequences using a hidden-Markov model (HMM) algorithm.

::DEVELOPER

Whitehead Institute for Biomedical Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PLAAC

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 13. pii: btu310. [Epub ahead of print]
PLAAC: a web and command-line application to identify proteins with Prion-Like Amino Acid Composition.
Lancaster AK1, Nutter-Upham A1, Lindquist S2, King OD3.

SNPAAMapper 2.0 – A SNP Amino Acid Mapping tool

SNPAAMapper 2.0

:: DESCRIPTION

SNPAAMapper is a downstream variant annotation program that can effectively classify variants by region (e.g. exon, intron, etc), predict amino acid change type (e.g. synonymous, non-synonymous mutation, etc), and prioritize mutation effects (e.g. CDS versus 5’UTR, etc).

::DEVELOPER

Computational Biology Lab at Indiana State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • PErl

:: DOWNLOAD

  SNPAAMapper

:: MORE INFORMATION

Citation

Bioinformation. 2013 Oct 16;9(17):870-2. doi: 10.6026/97320630009870. eCollection 2013.
SNPAAMapper: An efficient genome-wide SNP variant analysis pipeline for next-generation sequencing data.
Bai Y1, Cavalcoli J.

PaPI – Pseudo Amino Acid Composition to Score human Protein-coding Variants

PaPI

:: DESCRIPTION

PaPI is a new machine-learning approach to classify and score human coding variants by estimating the probability to damage their protein-related function.

::DEVELOPER

laboratorio di Bioinformatica e Biologia Sintetica – Univ. of Pavia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PaPI: pseudo amino acid composition to score human protein-coding variants.
Limongelli I, Marini S, Bellazzi R.
BMC Bioinformatics. 2015 Apr 19;16(1):123. doi: 10.1186/s12859-015-0554-8.

BiasViz 2 – Protein Amino Acid Bias Analysis Applet

BiasViz 2

:: DESCRIPTION

BiasViz can be used to look at the composition of amino acids within a sliding window given a multiple sequence alignment. The window size and amino acid(s) of interest can be modified and the results are displayed in real time, allowing the user to tweak both of these parameters to their liking. The values can also be downloaded as a CSV file which allows further visualization in a separate program such as Microsoft Excel.

::DEVELOPER

Matthew R. Huska

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 BiasViz

:: MORE INFORMATION

Citation

BiasViz: visualization of amino acid biased regions in protein alignments.
Huska MR, Buschmann H, Andrade-Navarro MA.
Bioinformatics. 2007 Nov 15;23(22):3093-4. Epub 2007 Oct 6.

MassShiftFinder 1.09 – Blind search for Post-translational Modifications and Amino Acid Substitutions

MassShiftFinder 1.09

:: DESCRIPTION

MassShiftFinder is a software tool for doing blind search using peptide mass fingerprints from two proteases with different cleavage specificities. The algorithm relies on overlapping peptides for the two proteases used, and can indicate both modifications and amino acid substitutions. The method can help restrict the area where the modification has occurred.

::DEVELOPER

The Proteomics Unit at the University of Bergen (PROBE)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

 MassShiftFinder

:: MORE INFORMATION

Citation

BMC Res Notes. 2008 Dec 19;1:130.
Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases.
Barsnes H, Mikalsen SO, Eidhammer I.

SIFT 6.2.1 – Amino Acid Substitution Affects Protein Function

SIFT 6.2.1

:: DESCRIPTION

SIFT (Sorting Intolerant From Tolerant) is a program for predicting whether an amino acid substitution affects protein function, based on sequence homology and the physical properties of amino acids. It is one of several programs using sequence information for this purpose.

::DEVELOPER

Fred Hutchinson Cancer Research Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  SIFT

:: MORE INFORMATION

Citation:

Ng PC, Henikoff S. 2002.
Accounting for human polymorphisms predicted to affect protein function.
Genome Research 12:436-446. doi:10.1101/gr.212802

iPAC 1.37.0 – Identification of Protein Amino acid mutation Clustering

iPAC 1.37.0

:: DESCRIPTION

iPAC finds mutation clusters on the amino acid level while taking into account the protein structure.

::DEVELOPER

Zhao Hongyu’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 iPAC

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Jun 13;14:190. doi: 10.1186/1471-2105-14-190.
Utilizing protein structure to identify non-random somatic mutations.
Ryslik GA, Cheng Y, Cheung KH, Modis Y, Zhao H.

DecoyDatabaseBuilder 1.5.47 – Generation of Decoy Sequences for Amino Acid Databases

DecoyDatabaseBuilder 1.5.47

:: DESCRIPTION

DecoyDatabaseBuilder is a module of the PeakQuant suite, it enables the generation of decoy sequences for amino acid databases.

::DEVELOPER

Medizinisches Proteom-Center, Medical Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • JRE

:: DOWNLOAD

 DecoyDatabaseBuilder

:: MORE INFORMATION

Citation

Proteomics. 2008 Mar;8(6):1129-37. doi: 10.1002/pmic.200701073.
An easy-to-use Decoy Database Builder software tool, implementing different decoy strategies for false discovery rate calculation in automated MS/MS protein identifications.
Reidegeld KA1, Eisenacher M, Kohl M, Chamrad D, Körting G, Blüggel M, Meyer HE, Stephan C.

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