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Links tagged with 'open reading frames'

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Found 30 links

Displaying 15 links

3D-pssmTool Content

http://www.sbg.bio.ic.ac.uk/~3dpssm/index2.html

Protein > 3-D Structure Prediction

Protein fold recognition using 1d and 3d sequence profiles coupled with secondary structure and solvation potential information.

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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome bacterial proteins computational biology factual databases flavoproteins integrases molecular models molecular sequence data mycoplasma open reading frames protein folding proteins proteome reproducibility of results retroviridae proteins ribonuclease h secondary protein structure sequence alignment solvents structure-activity relationship

AMIGeneTool Content

http://www.genoscope.cns.fr/agc/tools/amigene/Form/form.php

DNA > Gene Prediction
Model Organisms > Microbes

Annotation of MIcrobial Genes (AMIGene) is gene prediction server that can identify coding sequences in microbes.

NAR Web Server Issue 2003
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tagsbacterial dna bacterial genes dna sequence analysis markov chains open reading frames

BAGELDatabase Content

http://bioinformatics.biol.rug.nl/websoftware/bagel/bagel_start.php

DNA > Gene Prediction
Model Organisms > Microbes

BActeriocin GEnome mining tooL (BAGEL) identifies putative bacteriocin ORFs (antimicrobial peptides) based on a database containing information about known bacteriocins and adjacent genes involved in bacteriocin activity.

NAR Web Server Issue 2006
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tagsamino acid motifs bacterial genome bacteriocins genetic databases genomics multigene family open reading frames

BAGEL2Tool Content

http://bagel2.molgenrug.nl

DNA > Gene Prediction
Model Organisms > Microbes

BAGEL2 (BActeriocin GEnome mining tooL) identifies putative bacteriocins on the basis of conserved domains, physical properties and genomic context. Improved genome mining capacity from BAGEL.

NAR Web Server Issue 2010
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tagsamino acid motifs anti-bacterial agents bacterial genome bacteriocins data mining genomics open reading frames

BROPResource Content

http://brop.org/

Expression > Transcript Expression Analysis
Model Organisms > Microbes

The Bioinformatics Resource for Oral Pathogens (BROP) contains tools for genomics of oral pathogens including Genome Viewer, GOAL (genome wide ORF alignment), an oral pathogen microarray database, an entrez counter, oral pathogen specific BLAST, and a codon usage database.

NAR Web Server Issue 2005
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tagsbacteria bacterial capsules bacterial genes bacterial genome bacterial polysaccharides bacterial proteins biological evolution computational biology dna transposable elements fungal genome genetic databases genetic variation genomic islands genomics horizontal gene transfer integrases mouth oligonucleotide array sequence analysis open reading frames operon porphyromonas gingivalis sequence alignment streptococcus mutans transfer rna virulence virulence factors

Candida Genome DatabaseDatabase Content

http://www.candidagenome.org/

Model Organisms > Databases

The Candida Genome Database provides online access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. Two tools have been added to the DB. The Biochemical Pathways tool provides visualization of metabolic pathways and analysis tools that facilitate interpretation of experimental data, including results of large-scale experiments, in the context of Candida metabolism. Textpresso for Candida allows searching through the full-text of Candida-specific literature, including clinical and epidemiological studies.

NAR Database Issue 2010
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tagscandida albicans computational biology fungal dna fungal genes fungal genome genetic databases nucleic acid databases open reading frames protein databases tertiary protein structure

CyanoBaseDatabase Content

http://genome.kazusa.or.jp/cyanobase

Model Organisms > Databases

CyanoBase is the genome database for cyanobacteria, which are model organisms for photosynthesis. The database houses cyanobacteria species information, complete genome sequences, genome-scale experiment data, gene information, gene annotations and mutant information.

This content is being maintained by mn.

NAR Database Issue 2010
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tagsbacterial genome computational biology genetic databases nucleic acid databases open reading frames protein databases synechocystis tertiary protein structure

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 GenomesDatabase Content

http://www.ensemblgenomes.org

Model Organisms > Databases

Ensembl Genomes is a new portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualisation platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualised in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site.

NAR Database Issue 2010
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tagsanimals anopheles gambiae bacterial genome classification computational biology fungal genome gene expression genetic databases genetic polymorphism genome humans invertebrates nucleic acid databases open reading frames plant genome search engine single nucleotide polymorphism tertiary protein structure

FrameDTool Content

http://genopole.toulouse.inra.fr/bioinfo/FrameD/FD

DNA > Gene Prediction

FrameD is a program that predicts coding regions in prokaryotic and eukaryotic sequences that may contain frameshifts.

NAR Web Server Issue 2003
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tagsamino acid sequence homology bacterial genome complementary dna dna sequence analysis eukaryotic cells expressed sequence tags frameshift mutation gc rich sequence genes open reading frames

GlimmerTool Content

http://cbcb.umd.edu/software/glimmer/

DNA > Gene Prediction

Gene Locator and Interpolated Markov Modeler; this prokaryote-gene finding tool is the primary microbial gene finder used at TIGR; free (including source code) with registration for non-commercial use.

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tagsalgorithms animals artifacts bacterial dna bacterial genes bacterial genome base sequence chromosome mapping decapodiformes dna sequence analysis genetic models genetic techniques haemophilus influenzae helicobacter pylori markov chains open reading frames prochloron reproducibility of results sensitivity and specificity sequence alignment symbiosis

H-InvDBDatabase Content

http://www.h-invitational.jp/

Human Genome > Databases

The H-Invitational Database (H-InvDB) is a comprehensive annotation resource of human genes and transcripts. The latest release of H-InvDB (release 6.2) provides the annotation for 219,765 human transcripts in 43,159 human gene clusters based on human full-length cDNAs and mRNAs. H-InvDB now provides several new annotation features, such as mapping of microarray probes, new gene models, relation to known ncRNAs and information from the Glycogene database. H-InvDB also provides useful data mining resources-'Navigation search', 'H-InvDB Enrichment Analysis Tool (HEAT)' and web service APIs.

This content is being maintained by cyamasak.

NAR Database Issue 2010
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tagsalternative splicing complementary dna computational biology genes genetic databases genetic models genetic polymorphism human genome humans messenger rna microsatellite repeats multigene family nucleic acid databases oligonucleotide array sequence analysis open reading frames single nucleotide polymorphism tertiary protein structure

IBM Bioinformatics and Pattern Discovery GroupTool Content

http://cbcsrv.watson.ibm.com/Tspd.html

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

NAR Web Server Issue 2003NAR Web Server Issue 2004
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals anti-infective agents archaeal genes archaeal genome automated pattern recognition bacterial genes bacterial genome base sequence biomedical engineering chemical dictionaries computational biology conserved sequence dna dna sequence analysis eukaryotic cells evaluation studies as topic factual databases gene expression genetic databases genome genomics histones humans initiator codon leghemoglobin molecular models molecular sequence data open reading frames peptides probability protein databases protein sequence analysis proteins proteome rna sequence analysis secondary protein structure sequence alignment sequence analysis ubiquitin viral genome

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

MADAPTool Content

http://ccg.vital-it.ch/madap/

DNA > Annotations
Expression > Gene Regulation
Human Genome > Annotations

MADAP is a clustering tool for the interpretation annotation data mapped onto complete or partial genome sequences. Initially developed for determining transcription start sites (TSS) by defining 5\' and 3\'ends of mRNA, MADAP also has utility in clustering other annotation data types (ChIP-chip data, for example).

NAR Web Server Issue 2007
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tagsalgorithms animals base sequence chromatin immunoprecipitation cluster analysis complementary dna computational biology dna primers eukaryotic cells expressed sequence tags genetic databases genetic promoter regions genome humans nucleic acid databases open reading frames response elements statistical models