Xpresso – Predicting Gene Expression levels from DNA Sequences

Xpresso

:: DESCRIPTION

Xpresso is a software suite whose goal is to predict gene expression levels and transcriptional activity from genomic sequences. It is trained using convolutional neural networks. Pre-trained models are available for the human, mouse, and several cell types for these species.

::DEVELOPER

Shendure Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows
  • Python
  • R

:: DOWNLOAD

Xpresso

:: MORE INFORMATION

Citation

Agarwal V, Shendure J.
Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks.
Cell Rep. 2020 May 19;31(7):107663. doi: 10.1016/j.celrep.2020.107663. PMID: 32433972.

XMatchView 1.2.5 – Visualize DNA Sequence Alignments.

XMatchView 1.2.5

:: DESCRIPTION

XMatchView is a python application designed to visualize DNA sequence alignments.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 XMatchView

:: MORE INFORMATION

AhoPro – Seach for Overrepresentation of Given motifs in DNA sequences, P-value calculation

AhoPro

:: DESCRIPTION

The project AhoPro was created to seach for overrepresentation of given motifs in DNA sequences and to search for motif cooccurrence. This could discover the synergy of transcription factors (TF), which usually takes place in regulatory modules of genes.

::DEVELOPER

Boeva lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WIndows

:: DOWNLOAD

 AhoPro

:: MORE INFORMATION

Citation:

Algorithms Mol Biol. 2007 Oct 10;2:13.
Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules.
Boeva V, Clément J, Régnier M, Roytberg MA, Makeev VJ.

Staden 2.0.0b11 – DNA Sequence Assembly , Editing and Analysis

Staden 2.0.0b11

:: DESCRIPTION

Staden is a fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) .

::DEVELOPER

Staden Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

Staden

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jul 15;26(14):1699-703. doi: 10.1093/bioinformatics/btq268. Epub 2010 May 30.
Gap5–editing the billion fragment sequence assembly.
Bonfield JK1, Whitwham A.

Rodger Staden, David P. Judge and James K. Bonfield.
Analysing Sequences Using the Staden Package and EMBOSS.
Introduction to Bioinformatics. A Theoretical and Practical Approach. Eds. Stephen A. Krawetz and David D. Womble. Human Press Inc., Totawa, NJ 07512 (2003)

N-score – Predict Nucleosome Positions from DNA Sequence information

N-score

:: DESCRIPTION

N-score is a wavelet analysis based model for predicting nucleosome positions from DNA sequence information.

::DEVELOPER

Guo-CHeng Yuan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Python/Matlab

:: DOWNLOAD

 N-score

:: MORE INFORMATION

Citation

Genomic sequence is highly predictive of local nucleosome depletion.
Yuan GC, Liu JS.
PLoS Comput Biol. 2008 Jan;4(1):e13

Crann 1.04 – Detect Adaptive Evolution in Protein-coding DNA Sequences

Crann 1.04

:: DESCRIPTION

Crann (pronounced ‘crown’) is the Irish word for ‘tree’.Crann has been developed in order to provide fast heuristic methods of detecting adaptive evolution in protein-coding genes. It is important that the user understands the advantages and limitations of these methods. It is also important for the user to know that the software is designed to perform a number of different tasks, however the interpretation of the results is left entirely to the user.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

Crann

:: MORE INFORMATION

Citation:

Creevey, C. and J. O. McInerney (2003).
CRANN: Detecting adaptive evolution in protein-coding DNA sequences
Bioinformatics (2003) 19: 1726.

RepeatMasker 4.1.0 – Screen DNA Sequences for Interspersed Repeats and Low Complexity DNA Sequences

RepeatMasker 4.1.0

:: DESCRIPTION

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including, cross_match, ABBlast/WUBlast, RMBlast and Decypher.

::DEVELOPER

RepeatMasker Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 RepeatMasker

:: MORE INFORMATION

Citation

Genome Res. 2008 Aug;18(8):1362-8. Epub 2008 May 23.
DupMasker: a tool for annotating primate segmental duplications.
Jiang Z, Hubley R, Smit A, Eichler EE.

TIGER – DNA Sequence Assembly

TIGER

:: DESCRIPTION

Tiger is a novel de novo assembly framework  which adapts to available computing resources by iteratively decomposing the assembly problem into sub-problems.

::DEVELOPER

IMPACT Reach Group (Illinois Microarchitecture Project using Algorithms and Compiler Technology)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 TIGER

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012;13 Suppl 19:S18. doi: 10.1186/1471-2105-13-S19-S18. Epub 2012 Dec 19.
TIGER: tiled iterative genome assembler.
Wu XL1, Heo Y, El Hajj I, Hwu WM, Chen D, Ma J.