The STACK Project

The STACK project aims to generate a comprehensive representation of the sequence of each of the expressed genes in the human genome by extensive processing of gene fragments to make accurate alignments, highlight diversity and provide a carefully joined set of consensus sequences for each gene.The STACK project is comprised of the STACKdb^TM human gene index, a database of virtual human transcripts, as well as stackPACK^TM, the tools used to create the database.

STACKdb v3.1

Now provided with a comprehensive full-length mRNA index and additional output reports containing potential alternate expression forms

STACKdb^TM

The STACKdb, Sequence Tag Alignment and Consensus Knowledgebase, is generated by processing EST and mRNA sequences obtained from GenBank through a pipeline consisting of masking, clustering, alignment and variation analysis steps. STACKdb is organized into 15 tissue-based categories and one disease category.The most recent release of the database is STACKdb v3.1. An up-to-date comprehensive mRNA index consisting of all mRNA sequences within HTD, MGC and RefSeq is provided with STACKdb v3.1 as a preview to the next release of STACKdb.

Accessing STACKdb:

Download the database for use at your own site (Academic institutions only).
Access or download STACKdb through your local EMBnet node (academic users only). To offer this service, EMBnet nodes must first complete a brief agreement with SANBI.

How does STACKdb data relate to:

Who uses STACKdb?

STACKdb is used by more than 150 institutions worldwide.
Check out a list of registered users.

stackPACK^TM

The stackPACK transcript reconstruction and variation analysis system allows the rapid and accurate processing of EST and mRNA data through a pipeline consisting of a series of steps including masking, loose clustering, assembly and alignment, alignment analysis for variation in transcripts and linking of non-overlapping clusters by clone ID. The system is unique due to its visualization tools and efficient data management, using a relational database. StackPACK can be accessed either through command line or through a web-based interface.

Check out some benchmarks of the performance of the d2_cluster algorithm used by stackPACK.

The most recent release of the software system for Intel-based PC Linux Red Hat, Silicon Graphics Irix, and Sun Solaris platforms is stackPACK v2.2. StackPACK v2.2 will be available for the IBM AIX platform shortly. The most recent release of the software system for the HP Tru64 platform is stackPACK v2.2.1.

NOTE: StackPACK v2.2.1 for HP Tru64 has the same functionality as stackPACK v2.2 for Intel-based PC Linux Red Hat, Silicon Graphics Irix, and Sun Solaris, and is a special release to accommodate many Tru64-specific issues that were encountered during development.

Accessing stackPACK:

Academic users may download stackPACK for use on a variety of computing platforms at your own site.

Who uses stackPACK?

StackPACK is the most widely used EST clustering system of its kind and is
employed by over 100 key research sites worldwide.
Check out a list of list of registered users.