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Unclassified tools | Comparative genomics

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…

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-GAEnsC
Algorithm

iRSpot-GAEnsC

Allows designation of DNA recombination. iRSpot-GAEnsC is a genetic algorithm…

Allows designation of DNA recombination. iRSpot-GAEnsC is a genetic algorithm (GA) -based ensemble model for identification of DNA recombination hotspots and coldspots. This method permits the…

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…

BLASTGrabber
Desktop

BLASTGrabber

Explores high-throughput BLAST output generated from large scale database…

Explores high-throughput BLAST output generated from large scale database searches. BLASTGrabber aims to facilitates visualization, analysis and selection of data. The software allows users to apply…

ODG
Desktop

ODG Omics Database Generator

Helps researchers to store and query data at genome-scales. ODG simplifies…

Helps researchers to store and query data at genome-scales. ODG simplifies knowledge transfer from prior work on model organisms and related species. This tool requires a database generation,…

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…

KinFin
Desktop

KinFin

Provides a user-friendly but rich analytical toolkit to review and interrogate…

Provides a user-friendly but rich analytical toolkit to review and interrogate orthology clustering. KinFin takes the output of standard orthology inference toolkits. It can be used to highlight…

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 to…

AlignMiner
Web

AlignMiner

Covers the gap in bioinformatic function by evaluating divergence in alignments…

Covers the gap in bioinformatic function by evaluating divergence in alignments that involve closely-related sequences. AlignMiner can identify putative single nucleotide polymorphisms (SNPs),…

GeneFamTaxScan
Desktop

GeneFamTaxScan

Allows users to investigate about absence of genes due to assembly errors,…

Allows users to investigate about absence of genes due to assembly errors, annotation errors or lineage-specific deletion.

Wotd
Desktop

Wotd

Provides an effective implementation of a top-down construction for suffix…

Provides an effective implementation of a top-down construction for suffix trees. Wotd is built on a space-efficient representation of suffix trees that requires 12 bytes per input character in the…

EVOPRINTER
Web

EVOPRINTER

Generates an evolutionary gene print (EvoP) of invariant DNA sequences as they…

Generates an evolutionary gene print (EvoP) of invariant DNA sequences as they appear in the reference DNA. EVOPRINTER superimposes multiple alignment readouts of individual reference-DNA versus…

Gblocks
Web

Gblocks

Selects blocks following a reproducible set of conditions. Gblocks is a program…

Selects blocks following a reproducible set of conditions. Gblocks is a program that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more…

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…

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…

Deltarho-web
Web

Deltarho-web

Scores dinucleotide composition differences of individual sequence entries with…

Scores dinucleotide composition differences of individual sequence entries with a chosen representative host genome sequence. Deltarho-web compares the dinucleotide composition of an input sequence…

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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