> > cDNA, EST, SAGE

cDNA, EST, SAGE

Links to clone repositories, expression data, methods, and tools for expressed sequence tags (EST) and serial analysis of gene expression (SAGE) are found here.

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Found 38 links

Displaying 15 links

ACIDDatabase Content

http://bioinfo.thep.lu.se/acid.html

Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE

The Array Clone Information Database (ACID) is a searchable resource for information about human, mouse, and rat cDNA clones. Each clone contains information about the assigned UniGene cluster(s), location in the full-length transcript, assigned gene ontology terms and position in the genome assembly.

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tagsanimals chromosome mapping database management systems genetic databases human genome humans mice molecular cloning oligonucleotide array sequence analysis

ADGOTool Content

http://www.btool.org/ADGO2

Expression > Gene Set Analysis
Expression > cDNA, EST, SAGE

ADGO is a web tool that provides composite interpretations for microarray data comparing two sample groups. It also provides composite interpretations and enrichment analysis for lists of genes from diverse sources of biological information.

NAR Web Server Issue 2011
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tagsalgorithms biological models computer simulation documentation gene expression profiling oligonucleotide array sequence analysis protein databases proteins

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

Allen Brain AtlasDatabase Content

http://www.brain-map.org

Expression > cDNA, EST, SAGE
Model Organisms > Mouse and Rat

The Allen Brain Atlas (ABA) project has developed a web-based application designed to aid the intersection of neuroscience and genomics. The ABA Application enables users to access an extensive database of high resolution in situ hybridization (ISH) images from over 10,000 genes, reference atlases in both the sagittal and coronal planes, gene expression masks capturing the intensity of gene expression or signal, and the ability to search for gene expression by anatomic region.

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AntiHunter 2.0Tool Content

http://bio.ifom-ieo-campus.it/antihunter

Expression > Gene Regulation
Expression > cDNA, EST, SAGE

AnitHunter 2.0 is a tool to detect potential EST antisense transcripts within a given genomic region from the analysis of BLAST output.

NAR Web Server Issue 2005
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tagsalgorithms antisense rna dna sequence analysis expressed sequence tags genetic databases sequence alignment time factors

ASPicTool Content

http://t.caspur.it/ASPIC/

Expression > Splicing
Expression > cDNA, EST, SAGE
Sequence Comparison > Other Alignment Tools

Alternative Splicing Prediction (ASPic) can predict alternative splicing of user submitted genes based on comparative analysis of available transcript and genome data from a variety of species. Results include graphical and tabular views of the splicing patterns of full-length mRNA isoforms compatible with the detected splice sites of the genes as well as structural and functional annotations.

NAR Web Server Issue 2006
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tagsalgorithms alternative splicing animals base sequence benchmarking exons gene expression profiling genomics heterogeneous-nuclear ribonucleoproteins humans introns messenger rna molecular computers molecular models protein isoforms rna splice sites sequence alignment software design software validation

BabelomicsTool Content

http://www.babelomics.org

DNA > Annotations
Expression > Gene Regulation
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes

Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

This content is being maintained by juan_aguilar.

NAR Web Server Issue 2005NAR Web Server Issue 2006NAR Web Server Issue 2008NAR Web Server Issue 2010
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tagsalgorithms animals artificial intelligence binding sites chromosome mapping dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny proteomics rats sequence alignment systems biology systems integration transcription factors

Cancer Genome Anatomy ProjectTool Content

http://cgap.nci.nih.gov/

DNA > Sequence Polymorphisms
Expression > cDNA, EST, SAGE
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Model Organisms > Other Vertebrates

Goal is to determine the gene expression profiles of normal, precancer, and cancer cells; resources for human and mouse include ESTs, gene expression patterns, SNPs, cluster assemblies, cytogenetic information, and tools to query and analyze the data.

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tagsgene library human genome project humans neoplasms

DEEPTool Content

http://www.bioinf.med.uni-goettingen.de/services/deep/

Expression > Gene Regulation
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Protein > Interactions, Pathways, Enzymes

DEEP (Differential Expression Effector Prediction) is a tool that can identify effectors of specific expression profiles by combining gene expression data with biological expert knowledge about biomolecular interaction networks (provided by resources like TRANSPATH, for example).

NAR Web Server Issue 2007
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tagsalgorithms animals biological models computational biology computer simulation gene expression profiling genetic models humans phenotype protein interaction mapping signal transduction statistical data interpretation

DiscoverySpaceTool Content

http://www.bcgsc.ca/bioinfo/software/discoveryspace/

Expression > Gene Regulation
Expression > cDNA, EST, SAGE

DiscoverySpace is a tool for gene expression analyses and biological discovery.

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E2GTool Content

http://bibiserv.techfak.uni-bielefeld.de/e2g/

Expression > cDNA, EST, SAGE
Sequence Comparison > Other Alignment Tools

E2G is a tool that maps a large set of EST and cDNA sequences to a user-supplied genomic sequence. The use of pre-computed indexed data structures increases the efficiency of the sequence comparison process, allowing a large amount of data to be mapped within a reasonable timeframe.

NAR Web Server Issue 2004
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tagsbase sequence chromosome mapping complementary dna expressed sequence tags genomics sequence alignment

EGassemblerTool Content

http://egassembler.hgc.jp

DNA > Mapping and Assembly
Expression > cDNA, EST, SAGE

EGassembler is a pipeline for clustering and assembling sequence fragments from transcript (EST) data or from shotgun sequencing.

This content is being maintained by amasoudin.

NAR Web Server Issue 2006
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tagscomputational biology dna sequence analysis expressed sequence tags genomics

ENDEAVOURTool Content

http://www.esat.kuleuven.be/endeavour

Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE

ENDEAVOUR is a computational approach to prioritize candidate genes for further study. Users input training genes already known to be involved in the process under study and the candidate genes to prioritize. The web server supports multiple species and integrates multiple genomic data to generate the final prioritization. ENDEAVOUR has been benchmarked in silico and experimentally validated leading to the discovery of novel disease genes in several genetic diseases.

This content is being maintained by ltranche.

NAR Web Server Issue 2008
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tagsalgorithms animal models animals caenorhabditis elegans cell differentiation chromosome mapping computational biology drosophila melanogaster gene expression regulation genes genetic models genetic predisposition to disease humans mice rats roc curve sensitivity and specificity statistical models zebrafish

ESTExplorerTool Content

http://estexplorer.biolinfo.org

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

ESTExplorer is an automated suite of programs to pre-process, assemble and functionally annotate ESTs at both DNA and protein level.

NAR Web Server Issue 2007
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tagsanimals complementary dna computational biology consensus sequence dna sequence analysis expressed sequence tags female genetic databases genomics haemonchus humans male nucleic acid databases oligonucleotide array sequence analysis programming languages untranslated regions

GeMprospectorTool Content

http://cgi-www.daimi.au.dk/cgi-chili/GeMprospector/main

DNA > Tools For the Bench
Expression > cDNA, EST, SAGE
Model Organisms > Plants

GeMprospector is designed to find cross-species genetic marker candidates in legumes and grasses. GeMprospector automates PCR primer design based on multiple sequence alignments of submitted ESTs and their homologues in sequence databases from legumes or grasses.

NAR Web Server Issue 2006
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tagsbase sequence conserved sequence dna primers expressed sequence tags fabaceae genetic markers genetic polymorphism genomics nucleic acid databases poaceae polymerase chain reaction sequence alignment

Tags associated with subcategory 'Expression/cDNA, EST, SAGE'

humans gene expression profiling expressed sequence tags algorithms sequence alignment dna sequence analysis animals genomics chromosome mapping oligonucleotide array sequence analysis genetic databases mice computational biology complementary dna genes base sequence rats messenger rna gene library plants codon disease susceptibility automated pattern recognition classification cluster analysis plant genome hordeum markov chains nucleic acid databases host-parasite interactions plant dna peptides ascomycota tumor cell line artificial intelligence genetic promoter regions nucleic acid sequence homology genome conserved sequence poaceae fabaceae genetic markers genetic polymorphism nucleic acid conformation nucleic acid regulatory sequences protein sequence analysis middle aged reading frames time factors tissue distribution nucleic acid repetitive sequences x-ray crystallography genetic predisposition to disease neoplasm proteins sequence tagged sites reproducibility of results neoplasms dna restriction enzymes software validation software design molecular models protein isoforms rna splice sites gene expression genetic techniques protein interaction mapping factual databases dna database management systems molecular cloning pancreas polymerase chain reaction molecular computers introns species specificity saccharomyces cerevisiae molecular sequence data proteins sensitivity and specificity symbiosis protein biosynthesis phylogeny proteomics signal transduction human genome project heterogeneous-nuclear ribonucleoproteins exons benchmarking systems biology systems integration transcription factors neural networks (computer) statistical data interpretation open reading frames private sector public sector national institutes of health (u.s.) National Center for Biotechnology Information (NCBI) alternative splicing dna-binding proteins neoplasm antigens