repDNA 1.1.4 – Generate various modes of Feature Vectors for DNA Sequences

repDNA 1.1.4

:: DESCRIPTION

repDNA (Representations of DNAs) is a Python package for generating the widely used features reflecting the physicochemical properties and sequence-order effects of DNAs and nucleotides.

::DEVELOPER

Liu Lab, Harbin Institute of Technology Shenzhen Graduate School.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 repDNA 

:: MORE INFORMATION

Citation

repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects.
Liu B, Liu F, Fang L, Wang X, Chou KC.
Bioinformatics. 2014 Dec 10. pii: btu820.

CSSSCL 1.0 – A Taxonomic Classifier for DNA Sequences.

CSSSCL 1.0

:: DESCRIPTION

CSSSCL is a python package that uses Combined Sequence Similarity Scores for accurate taxonomic CLassification of long and short reads.

::DEVELOPER

CSSSCL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 CSSSCL

:: MORE INFORMATION

Citation:

CSSSCL: a python package that uses Combined Sequence Similarity Scores for accurate taxonomic CLassification of long and short sequence reads.
Borozan I, Ferretti V.
Bioinformatics. 2015 Oct 9. pii: btv587.

Possum – Detect Cis-elements in DNA Sequences

Possum

:: DESCRIPTION

Possum predicts cis-elements in DNA sequences using the standard method of Position Specific Scoring Matrices. It measures the resemblance of every sequence fragment to the chosen cis-element matrices by calculating log-likelihood ratio scores (base e), and returns high-scoring sequence fragments.

::DEVELOPER

Zlab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 Possum

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W420-3.
MotifViz: an analysis and visualization tool for motif discovery.
Fu Y, Frith MC, Haverty PM, Weng Z.

Cister – Find Motif Clusters in DNA Sequences

Cister

:: DESCRIPTION

Cister (Cis-element Cluster Finder) predicts regulatory regions in DNA sequences by searching for clusters of cis-elements.

::DEVELOPER

Zlab

:: SCREENSHOTS

Command Line

Web version:

:: REQUIREMENTS

  • Linux / SUN Solaris 8 / SGI/IRIX/ Alpha (Compaq Tru64 UNIX V5.0A)

:: DOWNLOAD

Cister

:: MORE INFORMATION

Citation

Frith, M. C., Hansen U. and Weng, Z.
Detection of cis-element clusters in higher eukaryotic DNA
Bioinformatics 2001 Oct;17(10):878-889.

ROVER 20050711 – Find Relatively Overrepresented Motifs in DNA Sequences

ROVER 20050711

:: DESCRIPTION

ROVER (Relative OVER-abundance of cis-elements) is a tool for determining if one or more of a group of transcription factors is likely to regulate a group of genes. It was designed for use with promoters from groups of genes that are suspected of being co-regulated, such as those from a microarray study. ROVER compares two groups of promoters (a suspected co-regulated group and a non-regulated group) by determining the relative over-abundance of likely binding sites for a particular Transcription Factor (TF) in one group versus the other. ROVER calculates the significance of any over-abundance of binding sites for each TF and reports a probability of its chance occurrence. This can be interpreted as the probability that a given TF regulates the group of genes in question. Likely binding sites are found by looking for high-scoring matches to a Position Specific Weight Matrix (PSSM), which represents known binding sites for a transcription factor. In addition to determining the significance of each TF, ROVER also provides the subset of sequences likely to be regulated by each TF and the specific significant binding sites.

::DEVELOPER

Zlab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • JAVA

:: DOWNLOAD

ROVER

:: MORE INFORMATION

Citation:

Haverty, PM., Hansen, U., Weng, Z. (2004) Computational Inference of Transcriptional Regulatory Networks from Expression Profiling and Transcription Factor Binding Site Identification. Nucleic Acids Research, Vol. 32, 179-188.

 

Clover 20120216 – Find Overrepresented Motifs in DNA Sequences

Clover 20120216

:: DESCRIPTION

Clover (Cis-eLement OVERrepresentation) is a program for identifying functional sites in DNA sequences. If you give it a set of DNA sequences that share a common function, it will compare them to a library of sequence motifs (e.g. transcription factor binding patterns), and identify which if any of the motifs are statistically overrepresented in the sequence set.

::DEVELOPER

Zlab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac OsX / Linux / SUN Solaris 8 / SGI/IRIX

:: DOWNLOAD

Clover

:: MORE INFORMATION

Citation:

Martin C Frith, Yutao Fu, Liqun Yu, Jiang-Fan Chen, Ulla Hansen, Zhiping Weng (2004). Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Research 32(4):1372-81.

 

LASTZ 1.04.03 – Program for Aligning DNA Sequences

LASTZ 1.04.03

:: DESCRIPTION

LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.

::DEVELOPER

Miller Lab at Penn State University Center for Comparative Genomics and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  LASTZ

:: MORE INFORMATION

Citation:

Harris, R.S. (2007)
Improved pairwise alignment of genomic DNA.
Ph.D. Thesis, The Pennsylvania State University.

CodonCode Aligner 9.0.2 – DNA Sequence Assembly & Alignment

CodonCode Aligner 9.0.2

:: 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

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