README for STACKdb v3.1.1                               January 2003


This version of STACKdb replaces STACKdb v3.1.

STACKdb v3.1.1 contains the same data as STACKdb v3.1 but is provided 
with the much improved stackPACK v2.2 viewing software. The updated 
viewing software includes new viewing and extraction functions that 
enable rapid simplified analysis and manipulation of alignments and 
alignment analyses. Data exchange with third-party programs is also 
simplified resulting in easier assessment of highlighted areas of 
potential interest.

The current release of STACKdb is based on all human EST and mRNA 
sequences from GB125.0, 24 August 2001, downloaded from NCBI as of 
25 August 2001. 1,761,079 new EST and 87,085 new mRNA sequences have 
been added to the STACKdb v3.0 data to form 270,515 clusters and 5,711 
clonelinks in total. The database is organized into 15 tissue-based 
categories and a disease category. In addition a comprehensive 
full-length mRNA index consisting of all mRNA sequences within HTD, 
MGC and RefSeq is provided with STACKdb v3.1.1 as a preview to the 
next release of STACKdb. 

The mRNA sequences within the STACKdb categories were assigned to one 
or more tissue categories using BLAST comparisons instead of relying 
on mRNA annotation. This more comprehensive mRNA assignment ensured 
superior supervised clustering and consensus sequences accuracy. 


STACKdb v3.1.1 has been produced with the stackPACK v2.1, v2.1.1 and 
v2.2 Transcript Reconstruction and Variation Analysis Management 
System. The following is provided for each of the STACKdb categories, 
including the mRNA index:
 - Relational database tables for use with the stackPACK v2.2 viewing 
   software, included with the release.
 - FastA files containing non-redundant sets of linked clusters, 
   clusters and singletons.
 - FastA files containing alternate consensus sequences.


Several documentation files exist for this release. To maximize 
STACKdb value and benefits, we recommend that you review these before 
using the database.
 - README		 This document.
 - Release Notes	 Details about the release, including 
                         statistics and any known problems.
 - Install Instructions	 Installation instructions for the database 
                         files. Please read these carefully.
 - Protocol 		 Protocol used for the generation of STACKdb 
                         v3.1.1
 - How To	         How to get the most from searching STACKdb 
                         v3.1.1 - an overview of the capabilities of 
                         the viewing and data management software.
 - Output Format	 Details about the output report formats.
 - TissueTree 		 Strategy for separating EST sequences into 
                         tissue categories.


We hope that the STACKdb gene expression and variation information 
proves valuable to your research efforts and that the more 
comprehensive mRNA assignment and provision of alternate consensus 
sequences enhance the utility of STACKdb.

Your feedback is valuable to us. Comments and suggestions for 
improvement can be mailed to the STACKdb production team: 
stackprod@egenetics.com 


Sincerely,

Jonathan Niekerk                                  Liza Groenewald
Genome Data Production Manager                    Product Manager