> Tag > Links tagged with 'nucleic acid repetitive sequences'

Links tagged with 'nucleic acid repetitive sequences'

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ACLAMEDatabase Content

http://aclame.ulb.ac.be/ [open in a new window]

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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.

links directory index: 22
TitlePublication YearGoogle Scholar Citation Count
ACLAME: a CLAssification of Mobile genetic Elements, update 2010201022
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/ [open in a new window]

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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.

links directory index: 276
TitlePublication YearGoogle Scholar Citation Count
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters200640
FibreHelix, a program for calculating the X-ray diffraction pattern of macromolecules with helical symmetry: application to DNA coiled coils20052
MREPATT: detection and analysis of exact consecutive repeats in genomic sequences20036
Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN2003107
PROMO: detection of known transcription regulatory elements using species-tailored searches2002121
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

GENSCANTool Content

http://genes.mit.edu/GENSCAN.html [open in a new window]

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DNA > Gene Prediction

Identification of complete gene structures in genomic DNA.

links directory index: 3198
TitlePublication YearGoogle Scholar Citation Count
Finding the genes in genomic DNA1998404
Prediction of complete gene structures in human genomic DNA19972794
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external linksLink on Wikipedia
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

IMCB - Fugu Genome ProjectTool Content

http://www.fugu-sg.org/ [open in a new window]

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Model Organisms > Databases
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.

links directory index: 1759
TitlePublication YearGoogle Scholar Citation Count
Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes20021097
Fugu: a compact vertebrate reference genome2000108
Generation and analysis of 25 Mb of genomic DNA from the pufferfish Fugu rubripes by sequence scanning199980
Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome1993474
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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 [open in a new window]

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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.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
Manipulating multiple sequence alignments via MaM and WebMaM20057
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 [open in a new window]

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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.

links directory index: 3841
TitlePublication YearGoogle Scholar Citation Count
MEME SUITE: tools for motif discovery and searching2009174
MEME: discovering and analyzing DNA and protein sequence motifs2006507
Meta-MEME: motif-based hidden Markov models of protein families1997223
An artificial intelligence approach to motif discovery in protein sequences: application to steriod dehydrogenases199757
The megaprior heuristic for discovering protein sequence patterns199628
ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool199697
The value of prior knowledge in discovering motifs with MEME1995492
Fitting a mixture model by expectation maximization to discover motifs in biopolymers19942263
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 base sequence binding sites biopolymers computer communication networks databases as topic dna dna sequence analysis evaluation studies as topic factual databases ferredoxins genetic databases humans hydroxysteroid dehydrogenases internet mammals markov chains molecular models molecular sequence data nucleic acid repetitive sequences protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment sequence analysis software software design stochastic processes streptomyces tertiary protein structure theoretical models transcription factors transcriptional regulatory elements user-computer interface

Non-B DBDatabase Content

http://nonb.abcc.ncifcrf.gov [open in a new window]

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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.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes20119
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

WebMAMTool Content

http://compbio.cs.sfu.ca/MAM.htm [open in a new window]

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Sequence Comparison > Analysis of Aligned Sequences

This is the web version of the Multiple alignment Manipulator (MaM), which 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.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
Manipulating multiple sequence alignments via MaM and WebMaM20057
NAR Web Server Issue 2005
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsexons genomics nucleic acid repetitive sequences phylogeny sequence alignment

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