:: 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
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: 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.
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: DOWNLOAD
:: 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
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Rahul Siddharthan,
“Sigma: multiple alignment of weakly-conserved non-coding DNA sequences“,
BMC Bioinformatics 7:143 (2006)
:: 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
:: DOWNLOAD
:: 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.
