PhyloCSF 20121028 / PhyloCSF++ v1.1.0 – Distinguish Protein-coding and Non-coding Regions

PhyloCSF 20121028 / PhyloCSF++ v1.1.0

:: DESCRIPTION

PhyloCSF is a method to determine whether a multi-species nucleotide sequence alignment is likely to represent a protein-coding region. PhyloCSF does not rely on homology to known protein sequences; instead, it examines evolutionary signatures characteristic to alignments of conserved coding regions, such as the high frequencies of synonymous codon substitutions and conservative amino acid substitutions, and the low frequencies of other missense and non-sense substitutions (CSF = Codon Substitution Frequencies).

PhyloCSF ++ is an efficient and parallelized C ++ implementation of the popular PhyloCSF method to distinguish protein-coding and non-coding regions in a genome based on multiple sequence alignments.

::DEVELOPER

Mike Lin / Christopher Pockrandt

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PhyloCSF / PhyloCSF ++

:: MORE INFORMATION

Citation

Pockrandt C, Steinegger M, Salzberg SL.
PhyloCSF ++: A fast and user-friendly implementation of PhyloCSF with annotation tools.
Bioinformatics. 2021 Nov 4:btab756. doi: 10.1093/bioinformatics/btab756. Epub ahead of print. PMID: 34734986.

Lin MF, Jungreis I, and Kellis M (2011).
PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions.
Bioinformatics (2011) 27 (13): i275-i282.

SCORER 2.0 – Distinguish Parallel Dimeric and Trimeric Coiled-coil Sequences

SCORER 2.0

:: DESCRIPTION

SCORER, distinguishes coiled-coil oligomer states, and test it against the current standard, MultiCoil. The SCORER algorithm has been revised in two key respects: first, the statistical basis for SCORER is improved markedly. Second, the training set for SCORER has been expanded and updated to include only structurally validated coiled coils.

::DEVELOPER

WOOLFSON lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 SCORER

:: MORE INFORMATION

Citation

C.T. Armstrong, T.L. Vincent, P.J. Green and D.N. Woolfson,
SCORER 2.0: An algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences“.
Bioinformatics (2011) 27 (14): 1908-1914.

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