Bioinformatics Links Directory : 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.

GBA Server - (Found July 2, 2008 )

The GBA Server is an EST-based gene expression profiling and analysis platform. It implements the GBA (Guilt-by-Association) algorithm and, given a UniGene cluster, can be used to find genes with similar expression patterns.
http://gba.cbi.pku.edu.cn

ESTExplorer - (Found July 2, 2008 )

ESTExplorer is an automated suite of programs to pre-process, assemble and functionally annotate ESTs at both DNA and protein level.
http://binf1.chem.mq.edu.au:8080/est_pipeline/wrapper_files/login_page_main

ALGGEN - (Found July 2, 2008 )

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.
http://alggen.lsi.upc.es/

Allen Brain Atlas - (Found July 2, 2008 )

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.
http://www.brain-map.org

AntiHunter 2.0 - (Found July 2, 2008 )

AnitHunter 2.0 is a tool to detect potential EST antisense transcripts within a given genomic region from the analysis of BLAST output.
http://bioinfo.crs4.it/AH2.0/

ASPic - (Found July 2, 2008 )

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

Babelomics - (Found July 2, 2008 )

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).
http://babelomics.bioinfo.cipf.es/

DEEP - (Found July 2, 2008 )

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

DiscoverySpace - (Found July 2, 2008 )

DiscoverySpace is a tool for gene expression analyses and biological discovery.
http://www.bcgsc.ca/bioinfo/software/discoveryspace/

E2G - (Found July 2, 2008 )

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