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Links tagged with 'base composition'

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CodonOTool Content

http://digbio.missouri.edu/software/index.html

DNA > Structure and Sequence Feature Detection
Model Organisms > General Resources

CodonO is a method for measuring synonymous codon usage bias within and across genomes.

NAR Web Server Issue 2007
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tagsarchaeal dna archaeal genome bacterial dna bacterial genome base composition codon computational biology computer simulation gc rich sequence genetic code genetic models genome species specificity

CorGenTool Content

http://corgen.molgen.mpg.de

DNA > Structure and Sequence Feature Detection

CorGenmeasures long-range correlations in DNA sequences and can generate random sequences with the same (or user-specified) correlation and composition parameters.

NAR Web Server Issue 2006
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tagsalgorithms base composition computational biology cytosine dna sequence analysis genomics guanine humans sequence alignment statistical data interpretation

GC-ProfileTool Content

http://tubic.tju.edu.cn/GC-Profile/

DNA > Structure and Sequence Feature Detection

GC-Profile is a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences.

NAR Web Server Issue 2006
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tagsalgorithms animals archaeal genome automated pattern recognition bacterial genome base composition base sequence chickens chromosome mapping cpg islands cytosine dna dna sequence analysis genetic models genomic islands genomics guanine isochores molecular sequence data sequence alignment statistical models

ILMTool Content

http://cic.cs.wustl.edu/RNA/

RNA > Structure Prediction, Visualization, and Design

Server which provides iterated loop matching and maximum weighted matching algorithms for pseudoknot containing RNA secondary structure prediction. Algorithms can apply thermodynamic and comparative information, and thus can be used for either aligned or individual sequences.

NAR Web Server Issue 2004
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tagsalgorithms bacillus subtilis bacterial rna base composition base pairing base sequence escherichia coli feedback molecular models molecular sequence data nucleic acid conformation nucleic acid sequence homology phylogeny reproducibility of results rna rna sequence analysis sensitivity and specificity sequence alignment theoretical models thermodynamics transfer rna

MfoldTool Content

http://mfold.rna.albany.edu/?q=mfold/download-mfold

RNA > Structure Prediction, Visualization, and Design

Predict RNA secondary structure from sequence; does not predict pseudoknots - see PKNOTS.

NAR Web Server Issue 2003
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tagsbase composition base sequence consensus sequence dna molecular models molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid denaturation nucleic acid hybridization nucleic acid repetitive sequences rna single-stranded dna thermodynamics

ModelTest SeverTool Content

http://darwin.uvigo.es/software/modeltest_server.html

DNA > Phylogeny Reconstruction

ModelTest is program for the selection the model of DNA evolution (nucleotide substitution) that best fits your data from phylogenetic analyses.

NAR Web Server Issue 2006
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tagsalgorithms base composition bayes theorem biological models dna dna sequence analysis genetic variation likelihood functions molecular evolution nucleotides online systems sequence alignment statistical models

OligoCalcTool Content

http://www.basic.northwestern.edu/biotools/OligoCalc.html

DNA > Tools For the Bench

OligoCalc calculates the physical properties of single- and double-stranded DNA and RNA molecules including melting temperature (multiple methods), concentration, molecular weight, and absorbance at 260 nanometers. OligoCalc can also account for 5’ and 3’ chemical modifications and predict potential hairpin loop formation.

NAR Web Server Issue 2007
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tagsalgorithms animals base composition chemical models computational biology dna humans oligonucleotides rna temperature

RNAfoldTool Content

http://www.tbi.univie.ac.at/cgi-bin/RNAfold.cgi

RNA > Structure Prediction, Visualization, and Design

Predict RNA secondary structure from sequence; note sequence length limit.

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tagsalgorithms alzheimer disease amyloid beta-protein precursor base composition base sequence catalytic rna codon humans molecular sequence data nucleic acid conformation thermodynamics

TRACTSTool Content

http://bioportal.weizmann.ac.il/tracts/tracts.html

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection

TRACTS calculates the frequencies, locations and lengths of all binary tracts (pairs of nucleotide combinations) in DNA sequences. Annotated output will include exon/intron regions and tract information.

NAR Web Server Issue 2003
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tagsbase composition base sequence dna dna sequence analysis humans p53 genes purines pyrimidines

TraFaCTool Content

http://trafac.cchmc.org/trafac/index.jsp

Expression > Gene Regulation
Sequence Comparison > Comparative Genomics

TraFaC (Transcription Factor Binding Site Comparison) is a tool that identifes regulatory regions using a comparative sequence analysis approach.

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tagsanimals base composition binding sites brain chemistry cd4 antigens conserved sequence dna helicases dna-binding proteins gene expression profiling genetic databases genetic promoter regions humans intestines lung mice multigene family nucleic acid regulatory sequences organ specificity proteins transcription factors untranslated rna xeroderma pigmentosum group d protein

TwinscanTool Content

http://genes.cs.wustl.edu/

DNA > Gene Prediction

Twinscan is a system for predicting gene-structure in eukaryotic genomic sequences. In order to make its predictions, Twinscan combines the information from predicted coding regions and splice sites with conserservation measurements between the target sequence and sequences from a closely related genome. Currently sequences from mammalian genomes, and those of Arabidopsis thaliana, C. elegans, C. briggsae and strains JEC21 and H99 of Cryptococcus neoformans can be processed using Twinscan.

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tagsalgorithms animals base composition base sequence chromosome mapping computational biology conserved sequence dna exons forecasting gc rich sequence genes genome human genome humans mice molecular evolution nucleic acid sequence homology predictive value of tests sensitivity and specificity sequence alignment statistical models synteny

Viral BioinformaticsTool Content

http://athena.bioc.uvic.ca/

Model Organisms > Other Organisms
Protein > Sequence Features
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Viral Bioinformatics provides access to viral genomes and a variety of tools for comparative genomic analyses.

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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome base composition base sequence biological models canada capripoxvirus chlamydophila pneumoniae cluster analysis computational biology computer systems database management systems dna dna sequence analysis documentation factual databases fuzzy logic genetic databases genome genomics humans molecular evolution molecular sequence data multigene family multimedia mutation nucleic acid databases nucleic acid regulatory sequences nucleotides open reading frames phylogeny poxviridae programming languages protein databases protein sequence analysis reference standards sequence alignment statistical data interpretation systems integration technology transfer thermoplasma vaccinia virus variola virus viral dna viral genes viral genome viral proteins