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)

DECIPHER 2.0.2 – Decipher & Manage DNA Sequences

DECIPHER 2.0.2

:: DESCRIPTION

DECIPHER (Database Enabled Code for Ideal Probe Hybridization Employing R) is a software toolset that can be used for deciphering and managing DNA sequences efficiently using the R statistical programming language.  The program is designed to be used with non-destructive workflows that guide the user through the process of importing, maintaining, analyzing, manipulating, and exporting a massive amount of DNA sequences.

::DEVELOPER

Erik Wright

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 DECIPHER

:: MORE INFORMATION

Citation

DesignSignatures: a tool for designing primers that yield amplicons with distinct signatures.
Wright ES, Vetsigian KH.
Bioinformatics. 2016 Jan 23. pii: btw047

ES Wright et al. (2011)
DECIPHER: A Search-Based Approach to Chimera Identification for 16S rRNA Sequences.”
Applied and Environmental Microbiology,

igrep – DNA Sequence Matching

igrep

:: DESCRIPTION

igrep is a fast CUDA implementation of agrep algorithm for approximate nucleotide sequence matching

::DEVELOPER

Hongjian Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Hongjian Li, Bing Ni, Man-Hon Wong, and Kwong-Sak Leung.
A Fast CUDA Implementation of Agrep Algorithm for Approximate Nucleotide Sequence Matching.
In Proceedings of the 9th IEEE Symposium on Application Specific Processors (SASP), pp.74-77, San Diego, United States, 5-6 June 2011. DOI: 10.1109/SASP.2011.5941082

DanQ – A Hybrid Convolutional and Recurrent Neural Network for predicting the function of DNA Sequences

DanQ

:: DESCRIPTION

DanQ is a hybrid convolutional and recurrent neural network model for predicting the function of DNA de novo from sequence.

::DEVELOPER

CBCL Lab (Computational Biology and Computational Learning) @ UCI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 DanQ

:: MORE INFORMATION

Citation

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences.
Quang D, Xie X.
Nucleic Acids Res. 2016 Apr 15. pii: gkw226.

EDSSI – Engineered DNA Sequence Syntax Inspector

EDSSI

:: DESCRIPTION

EDSSI is an online bioinformatics pipeline that checks for syntax errors through three steps. First, ORF prediction in input DNA sequences is done by GeneMark; next, homologous sequences are retrieved by BLAST; and finally, syntax errors in the protein sequence are predicted by using the SIFT algorithm.

:: DEVELOPER

Anderson Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

 EDSSI

:: MORE INFORMATION

Citation

ACS Synth Biol. 2014 Feb 21;3(2):91-6. doi: 10.1021/sb400176e. Epub 2014 Jan 3.
Engineered DNA sequence syntax inspector.
Hsiau TH1, Anderson JC.

ACT 13 – Display Pairwise Comparisons between DNA Sequences

ACT 13

:: DESCRIPTION

ACT ( Artemis Comparison Tool)  is a free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation.

::DEVELOPER

the Sanger Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Java

:: DOWNLOAD

ACT

:: MORE INFORMATION

Citation

Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG and Parkhill J
ACT: the Artemis Comparison Tool.
Bioinformatics (Oxford, England) 2005;21;16;3422-3

RepeatMasker 4.0.6 – Screen DNA Sequences for Interspersed Repeats and Low Complexity DNA Sequences

RepeatMasker 4.0.6

:: 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.

4Peaks 1.8 – View & Edit DNA Sequence Trace Files

4Peaks 1.8

:: DESCRIPTION

4Peaks helps molecular biologists to visualize and edit their DNA sequence trace 4Peaks renders your traces sharper, automatically translate your sequences, reads the most common sequence file formats, displays important sequence quality data too.

::DEVELOPER

Nucleobytes

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Mac OsX

:: DOWNLOAD

 4Peaks

:: MORE INFORMATION

CodonCode Aligner 6.0.2 – DNA Sequence Assembly & Alignment

CodonCode Aligner 6.0.2

:: DESCRIPTION

CodonCode Aligner is a program for sequence assembly, contig editing, and mutation detection, available for Windows and Mac OS X. Aligner is compatible with Phred-Phrap and fully supports sequence quality scores, while offering a familiar, easy-to-learn user interface.

::DEVELOPER

CodonCode Corporation

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Mac OsX

:: DOWNLOAD

CodonCode Aligner

:: MORE INFORMATION