Tag: DNA sequences

D-Tailor 20130924 – Automated Analysis and Design of DNA Sequences

D-Tailor 20130924

:: DESCRIPTION

D-Tailor (DNA-Tailor) is a fully extendable software framework for biological sequence analysis and multi-objective sequence design. D-Tailor permits the seamless integration of an arbitrary number of sequence analysis tools into a Monte-Carlo algorithm that evolves synthetic sequences towards user-defined goals.

::DEVELOPER

The Arkin laboratory 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows/ MacOsX
  • Python

:: DOWNLOAD

 D-Tailor

:: MORE INFORMATION

Bioinformatics. 2014 Jan 13.
D-Tailor: automated analysis and design of DNA sequences.
Guimaraes JC1, Rocha M, Arkin AP, Cambray G.

LEPSCAN 1.0.6 – Searching Latent Periodicity in DNA sequences

LEPSCAN 1.0.6

:: DESCRIPTION

LEPSCAN (LatEnt Periodicity SCANner) web server is intended for searching the DNA sequences possessing latent periodicity.

::DEVELOPER

Andrew Shelenkov, Bioengineering Centre of Russian Academy of Sciences

:: SCREENSHOTS

 N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Brief Bioinform. 2012 Mar;13(2):143-9. doi: 10.1093/bib/bbr044. Epub 2011 Jul 22.
LEPSCAN–a web server for searching latent periodicity in DNA sequences.
Shelenkov A1, Korotkov E.

RopeBWT2 r187 – Incremental construction of FM-index for DNA sequences

RopeBWT2 r187

:: DESCRIPTION

RopeBWT2 is an tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pseudo-BWT position by position, starting from the end of the sequences.

::DEVELOPER

Heng Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RopeBWT2

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Aug 8. pii: btu541.
Fast construction of FM-index for long sequence reads.
Li H.

makeCGI 1.3.4 – Finding CpG Islands from DNA Sequences

makeCGI 1.3.4

:: DESCRIPTION

makeCGI is an R software package to obtain CGI from a genome. It fits two HMMs on GC content and observed to expected CpG ratio iteratively and obtain posterior probabilities for genomic regions being CpG islands. The CpG islands are then defined by thresholding the posterior probabilities.

::DEVELOPER

Hao Wu, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /Linux/ MacOsX
  • R

:: DOWNLOAD

 makeCGI

:: MORE INFORMATION

Citation

Wu H, Caffo B, Jaffe HA, Feinberg AP, Irizarry RA (2010)
Redefining CpG Islands Using a Hierarchical Hidden Markov Model.
Biostatistics 11(3): 499-514.

findIR – Detection of Perfect Overlapping and Nested Inverted Repeats in DNA Sequences

findIR

:: DESCRIPTION

Palindrome (also known as findIR) is a MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences.

::DEVELOPER

Liang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • MatLab

:: DOWNLOAD

 Palindrome

:: MORE INFORMATION

Citation

A MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences.
Sreeskandarajan S, Flowers MM, Karro JE, Liang C.
Bioinformatics. 2013 Nov 30.

Virtual Ribosome 2.0 / dna2pep 1.1 – Translating DNA sequences to the corresponding Peptide Sequences

Virtual Ribosome 2.0 / dna2pep 1.1

:: DESCRIPTION

The Virtual Ribosome (dna2pep) is a comprehensive tool for translating DNA sequences to the corresponding peptide sequences.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

  dna2pep

:: MORE INFORMATION

Citation

Virtual Ribosome – a comprehensive translation tool with support for sequence feature integration.
Rasmus Wernersson.
Nucl. Acids Res. 2006 34: W385-W388

DNA-Crypt 2.1 – Encrypts files into DNA Sequences

DNA-Crypt 2.1

:: DESCRIPTION

DNA-Crypt is a cryptography tool which encrypts files into DNA sequences. These sequences can be transfered to bacteria or other organisms without influencing them. You can use cryptographic keys, like RSA, AES or Blowfish, or, for maximum security, you can use a one time pad with DNA Crypt.

::DEVELOPER

Heider Lab

:: SCREENSHOTS

DNA-Crypt

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 DNA-Crypt

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 May 29;8:176.
DNA-based watermarks using the DNA-Crypt algorithm.
Heider D, Barnekow A.

Segment 1.04 – Identifying Compositional Domains in DNA Sequences

Segment 1.04

:: DESCRIPTION

Segment is a heuristic segmentation algorithm for DNA sequences. The program divides a DNA sequence into compositionally homogeneous domains by iterating a local optimization procedure at a given statistical significance.

::DEVELOPER

The group of computational genomics and bioinformatics at Granada University (Spain)

:: SCREENSHOTS

Segment

:: REQUIREMENTS

  • Windows 

:: DOWNLOAD

 Segment

:: MORE INFORMATION

Citation:

Oliver JL, Román-Roldán R, Pérez J, Bernaola-Galván P. 1999.
SEGMENT: identifying compositional domains in DNA sequences.
Bioinformatics 15: 974-979

SeqClean 20110222 – Trim & Validation of ESTs or other DNA sequences

SeqClean 20110222

:: DESCRIPTION

SeqClean (Sequence Cleaner) is a script for automated trimming and validation of ESTs or other DNA sequences by screening for various contaminants, low quality and low-complexity sequences.

::DEVELOPER

The Gene Index Project

:: REQUIREMENTS

:: DOWNLOAD

 SeqClean

:: MORE INFORMATION

Citation:

An optimized procedure greatly improves EST vector contamination removal.
Chen YA, Lin CC, Wang CD, Wu HB, Hwang PI.
BMC Genomics. 2007 Nov 13;8:416.