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Links tagged with 'nucleic acid repetitive sequences'

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ACLAMEDatabase Content

http://aclame.ulb.ac.be/

DNA > Databases

The ACLAME database is dedicated to the collection, analysis and classification of sequenced mobile genetic elements (MGEs, in particular phages and plasmids). Classifications are available at various levels of organization. At the gene/protein level, families group similar sequences that are expected to share the same function. Families of four or more proteins are manually assigned with a functional annotation using the GeneOntology and the locally developed ontology MeGO dedicated to MGEs. At the genome level, evolutionary cohesive modules group sets of protein families shared among MGEs. At the population level, networks display the reticulate evolutionary relationships among MGEs.

NAR Database Issue 2010
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tagsalgorithms bacterial genome bacteriophages computational biology genetic databases interspersed repetitive sequences nucleic acid databases nucleic acid repetitive sequences plasmids

ALGGENTool Content

http://alggen.lsi.upc.es/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.

NAR Web Server Issue 2003
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tagsalgorithms animals binding sites chickens chromosome mapping computational biology conserved sequence dna dna sequence analysis gene expression profiling genetic promoter regions genome genomics humans mice nucleic acid conformation nucleic acid databases nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology rats sequence alignment software design species specificity transcription factors x-ray crystallography

CRISPRFinderTool Content

http://crispr.u-psud.fr/Server/CRISPRfinder.php

DNA > Structure and Sequence Feature Detection
Model Organisms > Microbes

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Finder detects this family of direct repeats found in the DNA of many bacteria and archaea.

NAR Web Server Issue 2007
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tagsalgorithms archaeal genome bacterial genome chromosome mapping computational biology database management systems genetic databases intergenic dna nucleic acid repetitive sequences

GeneSeqerTool Content

http://www.plantgdb.org/search/misc/PublicPlantSeq.php

DNA > Gene Prediction
Expression > Splicing
Model Organisms > Plants

GeneSeqer is a method to identify exon/intron structure by splice site prediction and spliced alignment in plant genomes.

NAR Web Server Issue 2003
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tagsarabidopsis complementary dna computational biology dna sequence analysis expressed sequence tags gene components genetic databases genetic transcription genomics nucleic acid repetitive sequences plant dna plant genes plant genome plant proteins plants protein sequence analysis sequence alignment

GENSCANTool Content

http://genes.mit.edu/GENSCAN.html

DNA > Gene Prediction

Identification of complete gene structures in genomic DNA.

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tagsanimals dna dna sequence analysis exons genes genetic models genetic promoter regions genetic techniques genetic transcription human genome humans introns markov chains molecular sequence data nucleic acid repetitive sequences probability protein biosynthesis proteins rna splicing vertebrates

Gibbs Motif SamplerTool Content

http://ccmbweb.ccv.brown.edu/gibbs/gibbs.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs

Gibbs Motif Sampler allows you to identify motifs, conserved regions, in DNA or protein sequences. This tool can be applied for the detection of transcription factor binding sites (TFBS).

This content is being maintained by bbth.

NAR Web Server Issue 2003NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence animals bacterial dna bacterial genes bacterial genome bacterial outer membrane proteins base sequence binding sites biological evolution carrier proteins chemical models computational biology consensus sequence dna sequence analysis escherichia coli factual databases gammaproteobacteria gene expression regulation genetic models genetic transcription genetic variation helix-loop-helix motifs homology human genome humans markov chains mice molecular sequence data monte carlo method nonparametric statistics nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology phylogeny protein binding protein prenylation secondary protein structure sequence alignment skeletal muscle statistical models transcription factors transcription initiation site transferases

IMCB - Fugu Genome ProjectTool Content

http://www.fugu-sg.org/

Model Organisms > Fish

Lots of information on fugu including complete draft sequence, annotations, comparative vertebrate genomics, phylogenies, publications, and information about the fugu genome project; has some very useful tools including annotation tools, an Ensembl mirror, and BLAST.

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tagsanimals base sequence biological evolution computational biology conserved sequence cosmids dna dna sequence analysis dna transposable elements exons factual databases fish proteins fishes gene duplication gene library gene order genetic models genome genomics human genome humans introns japan mammals microsatellite repeats molecular evolution molecular sequence data nucleic acid repetitive sequences open reading frames phylogeny physical chromosome mapping poisonous fishes proteins proteome research satellite dna sequence alignment synteny takifugu vertebrates

MaMTool Content

http://compbio.cs.sfu.ca/MAM.htm

Sequence Comparison > Analysis of Aligned Sequences

The Multiple alignment Manipulator (MaM) takes a multiple alignment of genomic sequences as input and calculates the locations of exons, common repeat elements and unique regions based on user-selected programs/information. The graphical display also allows users to focus an assessment of sequence variation on the identified regions.

NAR Web Server Issue 2005
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tagsexons genomics nucleic acid repetitive sequences phylogeny sequence alignment

MEME SuiteTool Content

http://meme.nbcr.net/meme/intro.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs
Protein > Sequence Features
Sequence Comparison > Comparative Genomics

The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.

NAR Web Server Issue 2006NAR Web Server Issue 2009
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tagsalcohol dehydrogenase alcohol oxidoreductases algorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence automated pattern recognition automation bacterial proteins base sequence binding sites biopolymers chemical models consensus sequence dna dna sequence analysis entropy evaluation studies as topic factual databases ferredoxins genetic databases humans hydroxysteroid dehydrogenases mammals markov chains mathematical computing molecular models molecular sequence data nucleic acid repetitive sequences nucleic acid sequence homology oxidoreductases phylogeny protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment sequence analysis software design stochastic processes streptomyces tertiary protein structure theoretical models transcription factors transcriptional regulatory elements

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

Non-B DBDatabase Content

http://nonb.abcc.ncifcrf.gov

DNA > Databases

Non-B DB is a non-canonical (non-B) structure database database integrating annotations and analysis of non-B DNA-forming sequence motifs. The database provides alternative DNA structure predictions, including Z-DNA motifs, quadruplex-forming motifs, inverted repeats, mirror repeats and direct repeats and their associated subsets of cruciforms, triplex and slipped structures, respectively. The database also contains motifs predicted to form static DNA bends, short tandem repeats and homo(purine•pyrimidine) tracts that have been associated with disease. The database is accessed through query pages that produce results with links to the UCSC browser and a GBrowse-based genomic viewer.

NAR Database Issue 2011
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tagsanimals base sequence dna dogs genomics humans macaca mice nucleic acid conformation nucleic acid databases nucleic acid repetitive sequences pan troglodytes

SNPmaskerTool Content

http://bioinfo.ebc.ee/snpmasker/

DNA > Sequence Polymorphisms
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Expression > Transcript Expression Analysis
Human Genome > Sequence Polymorphisms

SNPmasker masks SNPs in a given sequence using information from the dbSNP database. This tool can also be used to mask repeat sequences. SNPmasker is primarily designed for masking the sequences before primer and probe design.

NAR Web Server Issue 2006
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tagsalleles animals dna primers genomics human genome humans mice nucleic acid databases nucleic acid probes nucleic acid repetitive sequences single nucleotide polymorphism

VISTATool Content

http://genome.lbl.gov/vista/index.shtml

DNA > Structure and Sequence Feature Detection
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.

NAR Web Server Issue 2004NAR Web Server Issue 2007
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tagsalgorithms animals base sequence binding sites cats cattle chickens chromosome mapping computational biology dna dna sequence analysis dogs exons gene expression profiling genome genomics human chromosomes human genome humans kinesin leukemia mice molecular evolution molecular sequence data nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology pan troglodytes papio phylogeny rabbits rats reproducibility of results sensitivity and specificity sequence alignment single nucleotide polymorphism swine takifugu time factors transcription factors untranslated regions zebrafish