U of I ESTIMA Songbird Start
GO Browser Sequence ID Gene Association Search by Blast Annotations Contig Viewer

Welcome to ESTIMA <Help File>

The Songbird EST project is a database for finding and retrieving gene sequences expressed in the zebra finch brain. To search the database, use the tools on the bar above (and described further at the bottom of this page).

This is the old songbird web site. Go to the new songbird website

ESTIMA:Songbird represents a still-evolving collection of zebra finch sequences and annotations, and has progressed so far through three generations (see History). A fourth generation of this database is now under development, and will be released here later in 2007.

ESTIMA:Songbird is part of a multi-institutional collaboration to develop genomics tools for songbird research. The project is funded by NIH grant RO1 NS045264 ("Songbird Neurogenomics Initiative," Principal Investigator: David Clayton). A formal description of this project and these annotations is in preparation: Replogle et al., "The Songbird Neurogenomics (SoNG) Initiative, a Shared Strategy for Gene Discovery and Analysis in Diverse Songbird Species."

CURRENT CONTENT

HISTORY

In the first generation of the database (2003), 2400 clones from the zebra finch brain cDNA library were produced by Prof. Juli Wade and Michigan State University and partially sequenced (single reads from 5' ends of inserts), yielding 1840 ESTs with a redundancy of 9.56%.

In the second generation (2004-2005), a new normalized cDNA library ("SB02") was produced at the Keck Center of the University of Illinois. More than 18,000 clones were partially sequenced (single reads from 5' ends of inserts), and a third cDNA library ("SB03") was then produced by subtractive depletion of these sequences from the SB02 library. More than 19,000 5' reads were obtained from SB03. In combination, 40,224 "filtered high quality" sequences were obtained from SB01, SB02 and SB03. Using standard clustering and "contig" algorithms, these ESTs were found to represent 17,878 non-redundant sequences. Those predicted gene products were annotated by BLAST sequence similarity searches against four external databases: TIGR Gallus gallus (chicken) EST, NCBI chicken unigene, Swissprot, NR.aa. Approximately 76% of the zebra finches ESTs had highly significant hits against the chicken EST collection.

To produce the third generation of this database (the present version), 5' and 3' end reads from ~14,000 zebra finch brain cDNAs were obtained from the Jarvis, Wada et al. group at Duke University and combined with the SB01-SB03 sequences above, to yield a total collection of 58,211 filtered high quality sequences. These assembled into 22,628 unique sequences and were annotated by the Bioinformatics Unit of the Keck Center. Assembly statistics can be found at http://titan.biotec.uiuc.edu/cgi-bin/ESTWebsite/estima_project_statistics?seqSet=songbird. We judge that these 58,211 ESTs represent products of about 15,000 genes.

Other annotation files and related resources can be found at:
http://titan.biotec.uiuc.edu/songbird/resources/


EST data can be searched and retrieved using the following methods:

Gene Ontology Browser
Search the database by entering a keyword to retrieve Gene Ontology recognized terms, and then view Songbird EST annotation for each of those terms. The Gene Ontology Consortium documentation is available at GO documentation.

Sequence ID
Enter an EST ID, GENBANK accession ID, or Contig ID to retrieve and download the sequences, view the sequence chromatograph, view the contig structure and the view the sequence annotation.

Gene Association
Search the database by entering a Sequence ID or Human Unigene Number or Gene Symbol to retrieve annotated ESTs for that ID.

Search by BLAST
Cut and paste one or more sequences to BLAST against several EST data sets.

EST Annotations
Search by description: Enter a familiar gene or protein name or descriptive term, to look for closely related sequences in the songbird EST collection. This function allows the searching on the description field of all records retrieved from the BLAST comparisons used in annotation.

Contig Viewer
Enter a contig id to view the consensus sequences that match with it.