STACK: Sequence Tag Alignment and Consensus Knowledgebase - PubMed (original) (raw)

STACK: Sequence Tag Alignment and Consensus Knowledgebase

A Christoffels et al. Nucleic Acids Res. 2001.

Abstract

STACK is a tool for detection and visualisation of expressed transcript variation in the context of developmental and pathological states. The datasystem organizes and reconstructs human transcripts from available public data in the context of expression state. The expression state of a transcript can include developmental state, pathological association, site of expression and isoform of expressed transcript. STACK consensus transcripts are reconstructed from clusters that capture and reflect the growing evidence of transcript diversity. The comprehensive capture of transcript variants is achieved by the use of a novel clustering approach that is tolerant of sub-sequence diversity and does not rely on pairwise alignment. This is in contrast with other gene indexing projects. STACK is generated at least four times a year and represents the exhaustive processing of all publicly available human EST data extracted from GenBank. This processed information can be explored through 15 tissue-specific categories, a disease-related category and a whole-body index and is accessible via WWW at http://www.sanbi.ac.za/Dbases.html. STACK represents a broadly applicable resource, as it is the only reconstructed transcript database for which the tools for its generation are also broadly available (http://www.sanbi.ac.za/CODES).

PubMed Disclaimer

Figures

Figure 1

Figure 1

Craw output for a whole-body index cluster displaying alternate gene isoforms of the fibulin gene. The blue box indicates the region capturing the fibulin-1B isoform whereas sequences capturing fibulin-1C are surrounded by a red box.

Figure 2

Figure 2

WebProbe, the STACK database extraction and viewing tool. The STACK tissue category is used as input to the ‘project name’ field that returns a list of all the clustered information.

Figure 3

Figure 3

An example linked entry for the olfactory tissue. The clusters contributing to the linked entry are displayed together with the ESTs comprising each cluster. A mouse click on a specific clusterID executes the download of the FASTA formatted multi-sequence file. The hyperlinks to the right of the clusterID provides for the display of detailed information pertaining to a cluster such as phrap alignments, consensus sequence and assembly analysis information. UniGene links to each EST are provided if they exist.

Similar articles

Cited by

References

    1. Houlgatte R., Mariage-Samson,R., Duprat,S., Tessier,A., Bentolila,S., Lamy,B. and Auffray,C. (1995) The Genexpress Index: a resource for gene discovery and the genic map of the human genome. Genome Res., 5, 272–304. - PubMed
    1. Schuler G.D. (1997) Pieces of the puzzle: expressed sequence tags. Nature Genet., 4, 332–333. - PubMed
    1. Quackenbush J., Liang,F., Holt,I., Pertea,G. and Upton,J. (2000) The TIGR Gene Indices: reconstruction and representation of expressed gene sequences. Nucleic Acids Res., 28, 141–145. Updated article in this issue: Nucleic Acids Res. (2001), 29, 159–164. - PMC - PubMed
    1. Hide W., Burke,J. and Davidson,D. (1994) Biological evaluation of d2, an algorithm for high-performance sequence comparison. J. Comput. Biol., 1, 199–215. - PubMed
    1. Burke J., Davidson,D. and Hide,W. (1999) d2_cluster: A validated method for clustering EST and full-length cDNA. Genome Res., 9, 1135–1142. - PMC - PubMed

MeSH terms

LinkOut - more resources