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.

GenoCanyon 1.0.3 – Predict Functional Non-coding Regions in Human Genome

GenoCanyon 1.0.3

:: DESCRIPTION

GenoCanyon is a whole-genome functional annotation approach based on unsupervised statistical learning.

::DEVELOPER

Hongyu Zhao’s Lab

:: SCREENSHOTS

GenoCanyon

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

GenoCanyon

:: MORE INFORMATION

Citation

A statistical framework to predict functional non-coding regions in the human genome through integrated analysis of annotation data.
Lu Q, Hu Y, Sun J, Cheng Y, Cheung KH, Zhao H.
Sci Rep. 2015 May 27;5:10576. doi: 10.1038/srep10576.