The STACKdb human gene index allows rapid simplified access and in-depth analysis to the ever-growing quantities of public EST and mRNA data. Over 5 million sequences are processed into hierarchically organized human transcript consensus sequences that are arranged and displayed to maximally reflect genetic polymorphisms and gene expression forms within several tissue-based categories and one disease category. In addition a comprehensive full-length mRNA index consisting of all mRNA sequences within HTD, MGC and RefSeq is provided with the latest release of STACKdb.

The peer-reviewed system is a unique resource for functional gene annotation, most significantly those genes associated with human disease, and is used by top research institutions worldwide to improve gene candidacy delivery.

A robust relational database architecture and intuitive data management and visualization tools link various consensus sequences, alignments and analyses. STACKdb further simplifies your in-house analysis pipeline with the inclusion of several data export functions can be accessed either from the web-based interface or from the command line - enabling smooth data exchange with third-party programs and easy integration with a broad range of bioinformatics tools.

Version 3.1 Now provided with: Comprehensive full-length mRNA index Additional output reports containing potential alternate expression forms

• mRNA-supervised EST clustering.
• Alternate expression forms capture. Each alternate expression form has its own consensus sequences and alignment.
• Web-based viewing software providing multiple views on cluster data with links to the Unigene database.
• Expression state organization.
• Easy data capture and extraction for further evaluation in external programs.
• Relational database backend

STACKdb is created with the stackPACK expression variation analysis and transcript reconstruction system. StackPACK has enhanced ability to detect cluster variation due to its maximum length transcript reconstruction and increased cluster membership. StackPACK's superior ability to elucidate alternative transcripts is fundamental in the selection of high quality unique clones for developing microarrays and the generation of gene expression profiles.

Disease gene discovery is enhanced by STACKdb's unique expression site organization, presenting the opportunity to rapidly explore transcript expression in specific tissues or subsets such as the disease-related sequences.

disease : adipose : brain : cochlea : connective : digestive : eye : genome : gland
heart : hemato-lymphatic : lung : olfactory : other : reproductive

No data is lost during processing and data from each of the stackPACK pipeline steps can be viewed and output. Each cluster is represented by the following:

• Primary and alternate consensus sequences.
• Phrap and final alignments for primary and alternate consensus sequences.
• Alignment analyses highlighting variation within the clusters.
• Clonelink consensus sequences.

STACKdb is able to output alignments in MSF, ClustalW and ACE formats allowing you to view alignments in the program of your choice without concerns for reformatting or parsing. In addition there is a list of pre-defined output reports, including a non-redundant output report, which can be selected and downloaded for further data evaluation or to create a searchable database of your clustering results. These reports can be generated from both the command line and the web-based interface.