SECISDesign – Design SECIS-Elements within the Coding Sequence

SECISDesign

:: DESCRIPTION

SECISDesign is a server for the design of SECIS-elements within the coding sequence of an mRNA with both structure and sequence constraints.

::DEVELOPER

Chair for Bioinformatics Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2005 Aug 1;21(15):3312-3. Epub 2005 May 26.
SECISDesign: a server to design SECIS-elements within the coding sequence.
Busch A1, Will S, Backofen R.

MinoTar – Predict microRNA Targets in Coding Sequence

MinoTar

:: DESCRIPTION

MinoTar predicts microRNA coding region targets by searching for highly conserved microRNA seed sites in coding regions. Conservation is judged conditionally on the observed amino acid evolution.

::DEVELOPER

the Perrimon Lab and Bonnie Berger‘s group at MIT.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WebServer

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Proc Natl Acad Sci U S A. 2010 Sep 7;107(36):15751-6. doi: 10.1073/pnas.1006172107.
Conserved microRNA targeting in Drosophila is as widespread in coding regions as in 3’UTRs.
Schnall-Levin M, Zhao Y, Perrimon N, Berger B.

CodingMotif – Determination of Overrepresented Nucleotide Motifs in Coding Sequences

CodingMotif

:: DESCRIPTION

CodingMotif calculates the exact motif P value under a Markov model that preserves the dinucleotide frequency as well as codon usage.

::DEVELOPER

The ChuangLab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 CodingMotif

:: MORE INFORMATION

Citation:

CodingMotif: exact determination of overrepresented nucleotide motifs in coding sequences.
Ding Y, Lorenz WA, Chuang JH.
BMC Bioinformatics. 2012 Feb 14;13:32. doi: 10.1186/1471-2105-13-32.

LaTcOm – Visualizing Rare Codon Clusters in Coding Sequence

LaTcOm

:: DESCRIPTION

LaTcOm is a new web tool designed for detecting and visualizing ‘rare codon clusters’ (RCC) using as input up to 50 coding/mRNA sequences in FASTA format.

::DEVELOPER

Bioinformatics Research Laboratory  (BRL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

LaTcOm: a web server for visualizing rare codon clusters in coding sequences.
Theodosiou A, Promponas VJ.
Bioinformatics. 2012 Feb 15;28(4):591-2. doi: 10.1093/bioinformatics/btr706.

CDS-plotcon – Detect Enhanced Conservation in Coding Sequences

CDS-plotcon

:: DESCRIPTION

The software package CDS-plotcon is specifically designed to search for conserved functional elements within CDSs. It uses an average model of the expected mutation patterns within CDSs (incorporating a nucleotide mutation matrix, amino acid substitution matrix, sequence divergence parameter t, mean synonymous:nonsynonymous substitution ratio V and phylogenetic tree; it can handle up to three overlapping CDSs in different read-frames). Using this, it calculates the expected number of mutations across the alignment in each column and compares this with the observed number of mutations. The results are plotted along the genome, and optionally passed through a sliding window (clipped) mean filter

::DEVELOPER

Andrew Firth

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 CDS-plotcon

:: MORE INFORMATION

codaln 1.0 / code2aln 1.2 – Progressive Multiple Alignments of Partially Coding Sequences.

codaln 1.0 / code2aln 1.2

:: DESCRIPTION

codaln is the successor of code2aln.codaln produces multiple nucleic acid alignments using information on coding and non-coding regions as part of the scoring function. This is done in order to prevent the problem of higher sequence divergency on the level of nucleic acids as compared to the underlying protein sequences in the case of coding at a certain region of the input nucleic acid sequences. The program allows plenty of user intervention to overrule the defaults.

::DEVELOPER

Bioinformatics Leipzig

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 codaln , code2aln

:: MORE INFORMATION

Citation

Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences
Roman R. Stocsits, Ivo L. Hofacker, Claudia Fried, Peter F. Stadler
BMC Bioinformatics 6: 160 [epub] (2005)