:: DESCRIPTION
SatFind – C-program for Finding Satellites in Genomes
::DEVELOPER
the Algorithmics and Genetics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2013 Apr 24;8(4):e62221. doi: 10.1371/journal.pone.0062221.
A satellite explosion in the genome of holocentric nematodes.
Subirana JA, Messeguer X.
:: DESCRIPTION
WebMOTIFS is an online tool for motif discovery, scoring, analysis, and visualization. It allows you to use different programs to search for DNA-sequence motifs, and to easily combine and evaluate the results.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W217-20.
WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches.
Romer KA, Kayombya GR, Fraenkel E.
:: 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
Sequence Analysis is a collage of coding projects which the author has written over the past several years for various clients in his work as a bioinformatics consultant
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
DNACLUST is a tool for clustering millions of short DNA sequences. The clusters are created in such a way that the “radius” of each clusters is no more than the specified threshold.
::DEVELOPER
the Center for Bioinformatics and Computational Biology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
BMC Bioinformatics. 2011 Jun 30;12:271.
DNACLUST: accurate and efficient clustering of phylogenetic marker genes.
Ghodsi M, Liu B, Pop M.
:: DESCRIPTION
BroadPeak is an algorithm for the identification of broad peaks from diffuse ChIP-seq datasets.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Feb 15;29(4):492-3. doi: 10.1093/bioinformatics/bts722. Epub 2013 Jan 7.
BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets.
Wang J, Lunyak VV, Jordan IK.
:: DESCRIPTION
Sunflower is an evolutionary model for promoters, analogous to the commonly used synonymous/nonsynonymous mutation models for protein-coding sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hoffman MM, Birney E. 2010.
An effective model for natural selection in promoters.
Genome Res. 20(5):685-692.
:: 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
TSRchitect allows the user to efficiently identify the putative promoter (the transcription start region, or TSR) from a variety of TSS profiling data types, including both single-end (e.g. CAGE) as well as paired-end (RAMPAGE, PEAT, STRIPE-seq).
::DEVELOPER
The Brendel Group @ Indiana University
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Raborn RT, Brendel VP.
Using RAMPAGE to Identify and Annotate Promoters in Insect Genomes.
Methods Mol Biol. 2019;1858:99-116. doi: 10.1007/978-1-4939-8775-7_9. PMID: 30414114.
:: DESCRIPTION
GoRAMPAGE is a workflow for promoter detection by 5′-read mapping.
::DEVELOPER
The Brendel Group @ Indiana University
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Raborn RT, Brendel VP.
Using RAMPAGE to Identify and Annotate Promoters in Insect Genomes.
Methods Mol Biol. 2019;1858:99-116. doi: 10.1007/978-1-4939-8775-7_9. PMID: 30414114.