ESTs

SGN houses EST collections for tomato, potato, pepper, eggplant and petunia and corresponding unigene builds. EST sequence data and cDNA clone resources greatly facilitate cloning strategies based on sequence similarity, the study of syntenic relationships between species in comparative mapping projects, and are essential for microarray technology.

Unigenes

SGN assembles and publishes unigene builds from these EST sequences. For more information, see Unigene Methods.

Maps and Markers

SGN has genetic maps and a searchable catalog of markers for tomato, potato, pepper, and eggplant.

Tomato Sequencing

SGN is the bioinformatics hub for the ongoing international project to fully sequence the euchromatic portion of the tomato genome. In this role, we house:

• a searchable catalog of tomato BACS
• more than 400,000 BAC end sequences from these BACs
• all BAC sequences used to assemble the tomato genome
• a Genome Browser for sequence annotations

Tools

SGN makes available a wide range of web-based bioinformatics tools for use by anyone, listed here. Some of our most popular tools include BLAST searches, the SolCyc biochemical pathways database, a CAPS experiment designer, an innovative Intron detection tool, an advanced Alignment Analyzer and browser for phylogenetic trees.

The data in SGN have been submitted by many different research groups around the world which are acknowledged on the corresponding pages on SGN. If you have data you would like to submit for display on SGN, please use the contact us web form, or email us at sgn-feedback\@sgn.cornell.edu.

For more information about SGN datasets, see the SGN Data Overview. Entire datasets can also be downloaded from our FTP site.

• We attempt to process all EST sequences directly from sequencing chromatograms using a custom pipeline developed at SGN. The sequences are assembled into unigenes using standard clustering software and in-house tools. A higher level of sequence quality is obtained when sequences are uniformly base-called and quality trimmed. Other software developed at SGN include the interactive comparative map viewer for genetic and physical maps, the Tree Browser and the Alignment Analyzer.
• Unigene Methods including assembly process, builds, cluster, and validation

• We have developed simple web interfaces for the SGN user-community to submit, annotate, and curate the Solanaceae locus and phenotype databases. Our goal is to share biological information, and have the experts in their field review existing data and submit information about their favorite genes and phenotypes.
• Please read more about the phenome database and how to submit information to SGN.

Staff

Interns

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Bioinformatics Analysts Robert Buels Joseph Gosselin Jonathan Leto Adri Mills Beth Skwarecki Dean Eckstrom Chris Carpita Marty Kreuter Chenwei Lin John Binns Teri Solow Nicholas Taylor Dan Ilut Robert Ahrens Mark Wright

Interns Jessica Jeffrey (2011) Dil Begum (2011) Samuel Moijueh (2011) Benjamin Gordon (2011) Jean Lee (2010) Dean Bobo (2010) Carolyn Ochoa (2010) Mallory Freeberg Carolyn Ochoa Johnathon Schulz Tim Jacobs Sasha Naydich Jessica Reuter Matthew Crumb Bob Albright Emily Hart Scott Bland Amarachukwu Enemuo

Benjamin Cole Caroline Nyenke Tyler Simmons Evan Herbst Emil Keyder Aseem Kohli Igor Dolgalev Miriam Wallace Jay Gadgil Jennifer Lee

• Bombarely A, Menda N, Tecle IY, Buels RM, Strickler S, Fischer-York T, Pujar A, Leto J, Gosselin J, Mueller LA (2010). The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucl. Acids Res. Oct 08, 2010. doi: 10.1093/nar/gkq866.
• Tecle IY, Menda N, Buels RM, van der Knaap E, Mueller LA (2010). solQTL: A Tool for QTL analysis, Visualization and Linking to Genomes at SGN Database. BMC Bioinformatics 2010, 11:525.
• Mueller LA, et al., (2009). A snapshot of the emerging tomato genome sequence. Plant Gen. March 2009 2:78-92; doi:10.3835/plantgenome2008.08.0005.
• Menda N, Buels RM, Tecle I, Mueller LA (2008). A community-based annotation framework for linking solanaceae genomes with phenomes. Plant Physiol. 2008 Aug;147(4):1788-99 (PMID: 18539779).
• Mueller LA, Mills AA, Skwarecki B, Buels RM, Menda N, Tanksley SD (2008). The SGN comparative map viewer. Bioinformatics. 2008 Feb 1;24(3):422-3.
• Mueller LA, Solow TH, Taylor N, Skwarecki B, Buels R, Binns J, Lin C, Wright MH, Ahrens R, Wang Y, Herbst EV, Keyder ER, Menda N, Zamir D, Tanksley SD (2005). The Sol Genomics Network. A Comparative Resource for Solanaceae Biology and Beyond. Plant Physiol 138(3):1310-7.
• Wu F, Mueller LA, Crouzillat D, Petiard V, Tanksley SD (2006). Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. Genetics. 2006 Nov;174(3):1407-20.
• Lin C, Mueller LA, Mc Carthy J, Crouzillat D, Petiard V, Tanksley SD (2005). Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts. Theor Appl Genet. 2005 Dec;112(1):114-30.

SGN gratefully acknowledges funding from the following funding sources:

	National Science Foundation (USA) #0820612 Tomato Chromosome 1 and 10 Sequencing, Coordination and Bioinformatics for the International Solanaceae Genome Initiative #9872617 - Development of Tools for Tomato Functional Genomics #9975866 - Tools for Potato Structural and Functional Genomics #0116076 - Exploitation of Tomato as a Model for Comparative and Functional Genomics #0421634 - Sequence and Annotation of the Euchromatin of Tomato. #0606595 - Characterization of the Tomato Secretome Using Integrated Functional and Computational Strategies
	USDA USDA CSREES, grant #2007-02777 SolCAP - Solanaceae Coordinated Agricultural Project
	Nestle Corporation SGN gratefully acknowledges a grant from the Nestle Corporation for generation, analysis and integration of Coffea canephora data.
	BARD BARD, grant #FI-370-2005 Bioinformatic links of simple and complex phenotypes with Solanaceae genomes.

Special thanks to the Cornell Biological Services Unit for making their compute clusters available for some of our analyses.

Some data on SGN was obtained from EU-SOL projects. Special thanks to our colleagues at EU-SOL.