RNAcode 0.3 – Analysis of Protein Coding Potential in Multiple Sequence Alignments

RNAcode 0.3

:: DESCRIPTION

RNAcode predicts protein coding regions in a a set of homologous nucleotide sequences. RNAcode relies on evolutionary signatures including synonymous/conservative mutations and conservation of the reading frame. It does not use any species specific sequence characteristics whatsoever and does not use any machine learning techniques.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RNAcode

:: MORE INFORMATION

Citation:

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.
Washietl S, Findeiss S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N.
RNA. 2011;17(4):578-94.

JDet 1.4.9 – Visualization of Function-related Conservation Patterns in multiple Sequence Alignments

JDet 1.4.9

:: DESCRIPTION

JDet is a multiplatform software for the interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. It contains the set of tools and features we consider critical for the daily work with this kind of data, and that previously were disseminated in different packages and web servers. The package includes two of our recently developed programs for extracting this kind of information from protein alignments. JDet can be extended via plugins to implement other methods or parse their results.

::DEVELOPER

[Computational Systems Biology Group @CNB-CSIC]

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 JDet

:: MORE INFORMATION

Citation

Thilo Muth, Juan A. Garcia-Martin, Antonio Rausell, David Juan, Alfonso Valencia & Florencio Pazos (2012).
JDet: Interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures.
Bioinformatics 28(4): 584-586.

OD-seq 20150813 – Outlier Detection in Multiple Sequence Alignments

OD-seq 20150813

:: DESCRIPTION

OD-seq is a practical and simple method to detect outliers in MSAs. It can also detect outliers in sets of unaligned sequences, but with reduced accuracy.

::DEVELOPER

Prof. Des Higgins

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 OD-seq

:: MORE INFORMATION

Citation

OD-seq: outlier detection in multiple sequence alignments.
Jehl P, Sievers F, Higgins DG.
BMC Bioinformatics. 2015 Aug 25;16:269. doi: 10.1186/s12859-015-0702-1.

IMgc – Generates Recombination-free Sequences from Recombination-rich Multiple Sequence Alignments

IMgc

:: DESCRIPTION

IMgc reads recombination-rich multiple sequence alignments, and returns the largest block containing no four-gamete violations.

::DEVELOPER

the Hammer Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ windows/MacOsX
  • Perl

:: DOWNLOAD

 IMgc

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Jul 15;23(14):1851-3.
Recombination-filtered genomic datasets by information maximization.
Woerner AE, Cox MP, Hammer MF.