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Unclassified tools | Comparative genomics

AGenDA
Web

AGenDA Alignment based Gene Detection Algorithm

Searches for conserved splice sites around peaks of local sequence similarity…

Searches for conserved splice sites around peaks of local sequence similarity in order to identify candidate exons from which complete gene models are then constructed. AGenDA is a homology-based…

iRSpot-TNCPseAA…
Web

iRSpot-TNCPseAAC

Identifies the recombination hotspots and coldspots with trinucleotide…

Identifies the recombination hotspots and coldspots with trinucleotide composition and pseudo amino acid components. iRSpot-TNCPseAAC is an online predictor in which a DNA sample was formulated by…

SPoRE
Desktop

SPoRE SPots of REcombination

Allows to model axis proteins, DNA double-strand breaks (DSB) localization and…

Allows to model axis proteins, DNA double-strand breaks (DSB) localization and density along chromosomes. SPoRE models axis proteins and DSB distributions based on genomic information. This framework…

STAG-CNS
Desktop

STAG-CNS Suffix Tree Arbitrary Gene number: Conserved Noncoding Sequence

Characterizes loss of conserved noncoding sequences associated with retained…

Characterizes loss of conserved noncoding sequences associated with retained duplicate genes from the ancient maize polyploidy. STAG-CNS integrates data from the promoters of conserved orthologous…

STS
Desktop

STS Suffix Tree Searcher

Allows the analysis of large numbers of unaligned long DNA sequences through…

Allows the analysis of large numbers of unaligned long DNA sequences through the application of disk-based partitioned suffix trees (based on MGB’s DiGeST). STS is designed as an easy-to-use tool…

NASC
Desktop

NASC Non Aligned Sequence Comparison

Performs different types of sequence comparison based in some distance…

Performs different types of sequence comparison based in some distance definitions between frequencies of L words or L tuples. NASC extracts a vector of counts from each sequence and each chosen…

iRSpot-PseDNC
Web

iRSpot-PseDNC

Identifies the recombination hotspots and coldspots with pseudo dinucleotide…

Identifies the recombination hotspots and coldspots with pseudo dinucleotide composition. iRSpot-PseDNC is an online predictor featured by formulating the DNA samples with a novel feature vector, the…

RF-DYMHC
Web

RF-DYMHC

Detects yeast meiotic recombination hotspots and coldspots from genome…

Detects yeast meiotic recombination hotspots and coldspots from genome sequences. RF-DYMHC is a random forest-based system, a prediction model and a machine-learning method. Compared with an…

ORFcurator
Web

ORFcurator

Facilitates the accurate and rapid identification of conserved gene clusters.…

Facilitates the accurate and rapid identification of conserved gene clusters. ORFcurator automates the process of discovering putative genes from publicly available genome sequence databases. It…

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