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Links tagged with 'species specificity'

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Found 24 links

Displaying 15 links

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

BLASTOTool Content

http://oxytricha.princeton.edu/BlastO/index.html

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

BLASTO (BLAST on Orthologous groups) is a modified BLAST tool for searching orthologous group data. It treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences.

NAR Web Server Issue 2007
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tagsalgorithms animals automated pattern recognition computational biology genetic databases genome genomics humans nucleic acid sequence homology phylogeny species specificity

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

COGsTool Content

http://www.ncbi.nlm.nih.gov/COG/

Protein > Domains and Motifs
Sequence Comparison > Comparative Genomics

Clusters of Orthologous Groups represent ancient conserved protein domains; use COGnitor tool to find COGS in sequence of interest.

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tagsamino acid sequence animals archaea archaeal genes archaeal proteins bacteria bacterial genes bacterial proteins caenorhabditis elegans conserved sequence drosophila melanogaster factual databases fungal genes fungal proteins genome methanococcus molecular evolution multigene family phylogeny proteins saccharomyces cerevisiae sequence alignment species specificity

DECATool Content

http://www.nactem.ac.uk/deca_details/start.cgi

Literature > Text Mining and Semantics

DECA is a species disambiguation system for biological named entities. The system will identify protein entities and disambiguate them according to species, by assigning NCBI Taxonomy organism IDs.

This content is being maintained by pthompson.

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tagsartificial intelligence data mining factual databases named entity recognition natural language processing species disambiguation species specificity terminology as topic text mining

EnsemblDatabase Content

http://www.ensembl.org

DNA > Databases
Model Organisms > Databases

The Ensembl project provides high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish.

NAR Database Issue 2010NAR Database Issue 2011
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tagsanimals anopheles gambiae classification computational biology genetic databases genetic variation genome genomics humans mice molecular sequence annotation nucleic acid databases nucleic acid regulatory sequences open reading frames protein databases rats search engine single nucleotide polymorphism species specificity tertiary protein structure zebrafish

Ensembl Genome BrowserTool Content

http://www.ensembl.org/

DNA > Annotations
Human Genome > Annotations
Model Organisms > General Resources
Model Organisms > Other Organisms

Website, MySQL server and perl API access to software system which produces and maintains automatic annotation on eukaryotic genomes.

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tagsanimals bacterial genome base sequence cattle computational biology database management systems dna sequence analysis dogs fungal genome gene expression genetic databases genetic polymorphism genetic variation genome genomics human genome humans invertebrates mice nucleic acid databases nucleic acid regulatory sequences plant genome protein databases proteins rats reference standards rna sequence alignment species specificity synteny systems integration tertiary protein structure transcriptional regulatory elements

INDELSCANTool Content

http://indelscan.genomics.sinica.edu.tw/IndelScan/

DNA > Annotations
Sequence Comparison > Analysis of Aligned Sequences

INDELSCAN is a tool for genome-wide identification of indels.

NAR Web Server Issue 2007
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tagsanimals base sequence computational biology genetic polymorphism human genome humans molecular sequence data mutation nucleic acid sequence homology saccharomyces cerevisiae sequence deletion single nucleotide polymorphism species specificity

iTOLTool Content

http://itol.embl.de

Protein > Phylogeny Reconstruction

The Interactive Tree of Life (iTOL) tool is useful for the display, manipulation and annotation of phylogenetic trees. In addition to standart tree viewer functions, it offers powerful annotation of phylogenetic trees with various additional datasets. Annotated trees can be exported into various graphical formats. An user account system is provided, offering easy tree management and sharing through workspaces and projects. Programmatic access is also available.

This content is being maintained by iletunic.

NAR Web Server Issue 2011
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tagsalgorithms animals chromosome mapping computational biology data display decision trees genetic databases horizontal gene transfer humans molecular evolution molecular sequence annotation phylogeny species specificity visualization

JCatTool Content

http://www.jcat.de/

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

JCAT (Java Codon Adaptation Tool) is a tool that can adjust the codon usage of an input sequence to the selected organism. Useful for improving the expression of foreign genes in hosts with different codon usage.

NAR Web Server Issue 2005
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tagsalgorithms animals caenorhabditis elegans codon escherichia coli gene expression pseudomonas aeruginosa recombinant proteins species specificity

MetaPath OnlineTool Content

http://scopes.biologie.hu-berlin.de/

Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes

MetaPath Online gives users access to an algorithm for network expansion. Starting with given metabolites, called seed compounds, the algorithm uses known information about metabolic reactions and pathways to expand the network and define scope. This systematic investigation of structure-function relationships of metabolic networks can offer evolutionary insights.

NAR Web Server Issue 2007
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tagsadenosine triphosphate algorithms animals archaea bacteria biological evolution biological models cell physiological phenomena chemical models coenzymes computational biology computer simulation energy metabolism eukaryotic cells factual databases gene expression profiling genetic models genetic variation glucose glycolysis humans inorganic chemicals kinetics metabolism molecular evolution nerve net organic chemicals phosphates phylogeny physiological adaptation protein biosynthesis proteins signal transduction species specificity substrate specificity

mGenomeSubtractorTool Content

http://bioinfo-mml.sjtu.edu.cn/mGS/

Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

mGenomeSubtractor performs mpiBLAST-based comparison of reference bacterial genomes against multiple user-selected genomes. Such in silico subtractive hybridization also allows for definition of species-specific gene pools and can be used to develop genomic arrays.

NAR Web Server Issue 2010
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tagsbacterial genes bacterial genome genomics oligonucleotide array sequence analysis sequence alignment species specificity

miPredTool Content

http://www.bioinf.seu.edu.cn/miRNA/

RNA > Functional RNAs

miPred (microRNA Predictor) can distinguish between real and pseudo microRNA precursors.

NAR Web Server Issue 2007
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tagsanimals base sequence computational biology computer simulation false positive reactions genome genomics humans messenger rna micrornas molecular sequence data nucleic acid conformation species specificity

MouseIndelDBDatabase Content

http://polybrowse.abcc.ncifcrf.gov/

Model Organisms > Databases

MouseIndelDB is an integrated database resource containing thousands of previously unreported mouse genomic indel (insertion and deletion) polymorphisms ranging from approximately 100 nt to 10 Kb in size. The database currently includes polymorphisms identified from our alignment of whole-genome shotgun sequence traces from four laboratory mouse strains mapped against the reference C57BL/6J genome using GMAP. They can be queried on a local level by chromosomal coordinates, nearby gene names or other genomic feature identifiers, or in bulk format using categories including mouse strain(s), class of polymorphism(s) and chromosome number. The results of such queries are presented either as a custom track on the UCSC mouse genome browser or in tabular format.

NAR Database Issue 2010
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tagsanimals computational biology genetic databases genetic models genetic polymorphism genome inbred c57bl mice mice nucleic acid databases protein databases species specificity

OSCARTool Content

http://biocomp.bioen.uiuc.edu/oscar/

Expression > Transcript Expression Analysis

OSCAR (Open System for Clustering Analysis) is a platform for cluster analysis of microarray data.

NAR Web Server Issue 2007
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tagsaging algorithms alzheimer disease animals biological models computational biology eye proteins genetic models homeodomain proteins humans insulin receptor nad(p)h dehydrogenase (quinone) neurons oligonucleotide array sequence analysis paired box transcription factors repressor proteins species specificity