csnpAnalysis 1.01 – PANTHER Coding SNP Analysis tool

csnpAnalysis 1.01

:: DESCRIPTION

 csnpAnalysis is a software to estimate the likelihood that a particular nonsynonymous (amino-acid changing) coding SNP will cause a functional impact to the protein.

::DEVELOPER

Paul D. Thomas

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 csnpAnalysis

:: MORE INFORMATION

Citation

Paul D. Thomas, et al. 2006.
Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools.
Nucl. Acids Res.34: W645-W650.

MACSE 2.05 – Multiple Alignment of Coding SEquences

MACSE 2.05

:: DESCRIPTION

MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.

::DEVELOPER

MACSE team

:: SCREENSHOTS

MACSE

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 MACSE

:: MORE INFORMATION

Citation

MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons.
Vincent Ranwez, Sébastien Harispe, Frédéric Delsuc, Emmanuel JP Douzery
PLoS One 2011, 6(9): e22594.

Magnolia – Classification of Coding and Noncoding RNAs

Magnolia

:: DESCRIPTION

Magnolia is a program suite to classify RNA sequences as protein-coding or noncoding genes by comparative analysis. It also produces advanced multiple sequence alignment for the data.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

MAGNOLIA: multiple alignment of protein-coding and structural RNA sequences
Arnaud Fontaine, Antoine de Monte, Helene Touzet
Nucleic Acids Research 36(Web-Server-Issue): 14-18 (2008)

SpeciesGeoCoder 1.1.0 / speciesgeocodeR 2.0-10- Coding of Species into user-defined units

SpeciesGeoCoder 1.1.0 / speciesgeocodeR 2.0-10

:: DESCRIPTION

SpeciesGeoCoder is a free software package for coding species occurrences into user-defined units for e.g. biogeographic analyses. using a combination of GIS polygons and altitudinal ranges.

speciesgeocodeR is an R-package for the preparation for geographic point occurrence data in biogeographic analyses.

::DEVELOPER

Antonelli Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux /  MacOsX
  • R / Python

:: DOWNLOAD

SpeciesGeoCoder / speciesgeocodeR

:: MORE INFORMATION

Citation

SpeciesGeoCoder: Fast Categorization of Species Occurrences for Analyses of Biodiversity, Biogeography, Ecology, and Evolution.
Töpel M, Zizka A, Calió MF, Scharn R, Silvestro D, Antonelli A.
Syst Biol. 2017 Mar 1;66(2):145-151. doi: 10.1093/sysbio/syw064.

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