Twine 20130802 – Find important Sequences in Cis-regulatory DNA

Twine 20130802

:: DESCRIPTION

Twine is a Java GUI with multiple graphical representations (‘Views’) of enhancer alignments that displays motifs, as IUPAC consensus sequences or position frequency matrices, in the context of phylogenetic conservation to facilitate cis-regulatory element discovery.

::DEVELOPER

Stephen Crews Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows/MacOsX/Linux
Java

:: DOWNLOAD

Twine

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):1690-2. doi: 10.1093/bioinformatics/btt264. Epub 2013 May 8.
Twine: display and analysis of cis-regulatory modules.
Pearson JC, Crews ST.

ExUTR 2017 – Prediction of 3′-UTR Sequences from NGS data

ExUTR 2017

:: DESCRIPTION

ExUTR is a practical and powerful tool that enables rapid genome-wide 3′-UTR prediction from massive RNA-Seq data

::DEVELOPER

ExUTR team,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

ExUTR

:: MORE INFORMATION

Citation

Huang Z, Teeling EC.
ExUTR: a novel pipeline for large-scale prediction of 3′-UTR sequences from NGS data.
BMC Genomics. 2017 Nov 6;18(1):847. doi: 10.1186/s12864-017-4241-1. PMID: 29110697; PMCID: PMC5674806.

SSCA – Sequences Selection for the Comparative Approach

SSCA

:: DESCRIPTION

SSCA is an algorithm for selecting combinations of RNA homologous sequences suitable for secondary structure predictions with the comparative approach.

::DEVELOPER

EVRY RNA – IBISC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Nov 28;8:464.
Predicting RNA secondary structure by the comparative approach: how to select the homologous sequences.
Engelen S1, Tahi F.

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

:: 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.

CNCI v2 – Distinguish Protein-coding and Non-coding Sequences

CNCI v2

:: DESCRIPTION

CNCI (Coding-Non-Coding Index) is a powerful signature tool by profiling adjoining nucleotide triplets to effectively distinguish protein-coding and non-coding sequences independent of known annotations.

::DEVELOPER

CNCI team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

CNCI

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Sep;41(17):e166. doi: 10.1093/nar/gkt646. Epub 2013 Jul 27.
Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts.
Sun L1, Luo H, Bu D, Zhao G, Yu K, Zhang C, Liu Y, Chen R, Zhao Y.

BASELINe 1.3 – Bayesian Estimation of Antigen-Driven Selection in Immunoglobulin Sequences

BASELINe 1.3

:: DESCRIPTION

BASELINe, a new computational framework for Bayesian estimation of Antigen-driven selection in Immunoglobulin sequences, provides a more intuitive means of analyzing selection by actually quantifying it.

::DEVELOPER

Kleinstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
R

:: DOWNLOAD

BASELINe

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Sep 1;40(17):e134. Epub 2012 May 27.
Quantifying selection in high-throughput Immunoglobulin sequencing data sets.
Yaari G1, Uduman M, Kleinstein SH.

Biogrep 1.0 – Optimised Version of Grep for matching Patterns against Sequences

Biogrep 1.0

:: DESCRIPTION

Biogrep is a tool designed to quickly match large sets of patterns against biosequence databases and is optimized for multi–processor computers. Biogrep uses standard POSIX extended regular expressions and can divide the pattern–matching task between a user–specified number of processors.

::DEVELOPER

The Bioinformatics & Metabolic Engineering Laboratory, Massachusetts Institute of Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Biogrep

:: MORE INFORMATION

Citation:

Kyle Jensen et. al. (2002);
“Biogrep: A multi-threaded pattern matcher for large pattern sets“

Seq-Gen 1.3.4 – Simulate the Evolution of Sequences along a Phylogeny

Seq-Gen 1.3.4

:: DESCRIPTION

Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. Thus large sets of replicate simulations can be easily created. It has been designed to be a general purpose simulator that incorporates most of the commonly used (and computationally tractable) models of molecular sequence evolution.

::DEVELOPER

Andrew Rambaut Group

:: SCREENSHOTS