> > 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 43 links

Displaying 15 links

ACIDDatabase Content

http://bioinfo.thep.lu.se/acid.html [open in a new window]

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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.

links directory index: 18
TitlePublication YearGoogle Scholar Citation Count
ACID: a database for microarray clone information200418
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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 [open in a new window]

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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.

links directory index: 28
TitlePublication YearGoogle Scholar Citation Count
ADGO 2.0: interpreting microarray data and list of genes using composite annotations.20113
ADGO: analysis of differentially expressed gene sets using composite GO annotation200625
NAR Web Server Issue 2011
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tagsalgorithms animals biological models cell differentiation computer simulation documentation gene expression profiling genes humans mice molecular sequence annotation oligonucleotide array sequence analysis protein databases proteins rats t-lymphocytes

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

Allen Brain AtlasDatabase Content

http://www.brain-map.org [open in a new window]

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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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external linksLink on Wikipedia

AntiHunter 2.0Tool Content

http://bio.ifom-ieo-campus.it/antihunter [open in a new window]

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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.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
AntiHunter 2.0: increased speed and sensitivity in searching BLAST output for EST antisense transcripts200511
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/ [open in a new window]

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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.

links directory index: 53
TitlePublication YearGoogle Scholar Citation Count
ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization200620
ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences200533
NAR Web Server Issue 2006
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BabelomicsTool Content

http://www.babelomics.org [open in a new window]

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

links directory index: 1271
TitlePublication YearGoogle Scholar Citation Count
Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling201045
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments200854
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments2006215
BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments2005204
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes2004753
NAR Web Server Issue 2005NAR Web Server Issue 2006NAR Web Server Issue 2008NAR Web Server Issue 2010
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Cancer Genome Anatomy ProjectTool Content

http://cgap.nci.nih.gov/ [open in a new window]

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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.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
The Cancer Genome Anatomy Project: power tools for cancer biologists20035
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tagsgene library human genome project humans neoplasms

DEEPTool Content

http://www.bioinf.med.uni-goettingen.de/services/deep/ [open in a new window]

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Expression > Gene Regulation
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Protein > Networks & Interactions, Pathways and 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).

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
DEEP--a tool for differential expression effector prediction20072
NAR Web Server Issue 2007
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diArk - a resource for eukaryotic genome researchDatabase Content

http://www.diark.org/ [open in a new window]

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DNA > Databases
Expression > cDNA, EST, SAGE

diArk is a database driven web application that is designed to store, organize, and present the most relevant information about completed genome projects and EST/cDNA data from eukaryotes.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
diArk 2.0 provides detailed analyses of the ever increasing eukaryotic genome sequencing data20111
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tagsassembly coverage cDNA EST eukaryote fasta genome genome sequencing metazoa phylogeny sequencing center sequencing project taxon taxonomy

DiscoverySpaceTool Content

http://www.bcgsc.ca/bioinfo/software/discoveryspace/ [open in a new window]

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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/ [open in a new window]

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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.

links directory index: 16
TitlePublication YearGoogle Scholar Citation Count
e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences200416
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 [open in a new window]

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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.

links directory index: 58
TitlePublication YearGoogle Scholar Citation Count
EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments200658
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 [open in a new window]

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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.

links directory index: 412
TitlePublication YearGoogle Scholar Citation Count
ENDEAVOUR update: a web resource for gene prioritization in multiple species200867
Gene prioritization through genomic data fusion2006345
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 [open in a new window]

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

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

links directory index: 166
TitlePublication YearGoogle Scholar Citation Count
ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform200750
A hitchhiker's guide to expressed sequence tag (EST) analysis2007116
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

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