StarORF – Identification of the Protein(s) Encoded within a DNA sequence

StarORF

:: DESCRIPTION

StarORF facilitates the identification of the protein(s) encoded within a DNA sequence. Using StarORF, the DNA sequence is first transcribed into RNA and then translated into all the potential ORFs (Open Reading Frame) encoded within each of the six translation frames (3 in the forward direction and 3 in the reverse direction).

:: DEVELOPER

The STAR program at MIT

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 StarORF

:: MORE INFORMATION

TAMO 20120321 – Analyze Transcriptional Regulation using DNA-sequence Motifs

TAMO 20120321

:: DESCRIPTION

TAMO  (Tools for Analysis of MOtifs) is developed around a unified motif representation of a position-specific scoring matrix (PSSM). Motif objects may be assembled from IUPAC-ambiguity codes, multiple sequence alignments, averages of other motifs, and matrices of frequencies or log-likelihood values. Motifs can printed, concatenated, indexed and sliced like text strings, or rendered as sequence logos. They can also be randomized, reverse-complemented, and recomputed using different assumptions about background base frequencies. Motifs can also store and report information about their origin, information content, and score. Finally, motifs can scan DNA sequences for instances of matching sites.

::DEVELOPER

The Fraenkel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 TAMO

:: MORE INFORMATION

Citation:

D. Benjamin Gordon, Lena Nekludova, Scott McCallum and Ernest Fraenke
TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs.
Bioinformatics. 2005 Jul 15;21(14):3164-5.

ThioFinder 1.2 – Identification of Thiopeptide Gene Clusters in DNA sequences

ThioFinder 1.2

:: DESCRIPTION

ThioFinder is a web-based tool  to rapidly identify thiopeptide biosynthetic gene cluster from DNA sequence using a profile Hidden Markov Model approach.

::DEVELOPER

Microbial Genomics and Bioinformatics Group, SKMML, SJT

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

PLoS One. 2012;7(9):e45878. doi: 10.1371/journal.pone.0045878.
ThioFinder: a web-based tool for the identification of thiopeptide gene clusters in DNA sequences.
Li J, Qu X, He X, Duan L, Wu G, Bi D, Deng Z, Liu W, Ou HY.

IMMpractical 1.2 – Markov Chain Models for Analysis of DNA Sequences

IMMpractical 1.2

:: DESCRIPTION

IMMpractical implements various Markov chain model-based methods for analysis of DNA sequences.Markov chain models are commonly used for content-based appraisal of coding potential in genomic DNA.

::DEVELOPER

The Brendel Group @ Indiana University

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

IMMpractical

:: MORE INFORMATION

Citation

Sparks, M.E., Brendel, V. and Dorman, K.S. (2007)
Markov model variants for appraisal of coding potential in plant DNA.
LNBI. 4463:394-405.

RHOM – Research of HOMogeneous regions in DNA sequences

RHOM

:: DESCRIPTION

RHOM (Research of HOMogeneous regions in DNA sequences) is software designed for the use of hidden Markov chain models for the segmentation of DNA sequences in homogeneous regions. R’HOM makes it possible to estimate a more realistic model of DNA sequence composition than a homogeneous Markov chain model and then to segment the sequence under this model. It has been used in particular to look for horizontal transfers in B. subtilis and to estimate models designed to calculate the significance of word counting. R’HOM has been developed in cooperation with the Laboratoire Statistique et Génome in Evry.

::DEVELOPER

SSB group.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RHOM

:: MORE INFORMATION

SPADS 1.0 – Spatial and Population Analysis of DNA Sequences

SPADS 1.0

:: DESCRIPTION

SPADS is a population genetics software computing several summary statistics from populations or groups of populations, and implementing two clustering algorithms to study the genetic structure of populations. SPADS has been specifically developed for the analysis of DNA sequences. The first aim of SPADS is to compute, on real datasets, the summary statistics computed by PhyloGeoSim on each simulated datasets.

::DEVELOPER

Evolutionary Biology & Ecology, Université Libre de Bruxelles

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 SPADS

:: MORE INFORMATION

Citation

SPADS 1.0: a toolbox to perform spatial analyses on DNA sequence datasets.
Dellicour S, Mardulyn P.
Mol Ecol Resour. 2013 Nov 11. doi: 10.1111/1755-0998.12200

seqRFLP 1.0.1 – Predicting RFLP from DNA sequences

seqRFLP 1.0.1

:: DESCRIPTION

seqRFLP includes functions for handling DNA sequences, especially simulated RFLP and TRFLP pattern based on selected restriction enzyme and DNA sequences.

::DEVELOPER

Jinlong Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 seqRFLP

:: MORE INFORMATION

Tiara 1.0.2 – a tool for DNA sequence Classification

Tiara 1.0.2

:: DESCRIPTION

Tiara is a deep-learning-based approach for identification of eukaryotic sequences in the metagenomic data powered by PyTorch.

::DEVELOPER

Institute of Evolutionary Biology, University of Warsaw

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

Tiara

:: MORE INFORMATION

Citation:

Karlicki M, Antonowicz S, Karnkowska A.
Tiara: Deep learning-based classification system for eukaryotic sequences.
Bioinformatics. 2021 Sep 27:btab672. doi: 10.1093/bioinformatics/btab672. Epub ahead of print. PMID: 34570171.

Sigma 2.0 BETA – Non-coding DNA Sequence Alignment

Sigma 2.0 BETA

:: DESCRIPTION

Sigma (Simple greedy multiple alignment) is an alignment program with a new algorithm and scoring scheme designed specifically for non-coding DNA sequence.This problem is now growing in importance with the increasing number of fully-sequenced species. In particular, studies of gene regulation seek to take advantage of comparative genomics, and recent algorithms (such as PhyloGibbs) for finding regulatory sites in phylogenetically-related intergenic sequence require alignment as a preprocessing step.

::DEVELOPER

RAHUL SIDDHARTHAN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Sigma

:: MORE INFORMATION

Citation:

Rahul Siddharthan,
Sigma: multiple alignment of weakly-conserved non-coding DNA sequences“,
BMC Bioinformatics 7:143 (2006)

TESS 1.0 – Predict Transcription Factor Binding Sites in DNA sequence

TESS 1.0

:: DESCRIPTION

TESS (Transcription Element Search System) reads (selected) PWMs (Partial Weight Matrices) from a file and predicts binding sites on DNA sequences read from another file.

::DEVELOPER

the Computational Biology and Informatics Laboratory at the University of Pennsylvania

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • C Compiler

:: DOWNLOAD

 TESS 

:: MORE INFORMATION

Citation:

Curr Protoc Bioinformatics. 2008 Mar;Chapter 2:Unit 2.6. doi: 10.1002/0471250953.bi0206s21.
Using TESS to predict transcription factor binding sites in DNA sequence.
Schug J.

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