Toolbar help

The toolbar is located on the upper portion of the screen on almost every page on the SGN site and provides an easy way to navigate the site. The toolbar consists of the SGN logo and a row of links that link to the main portions of the site. When the mouse passes over a link, a pull down menu is displayed (assuming you have JavaScript turned on). You can either click the main link or scroll down the menu to choose a menu item. If you are having problems with the toolbar, you may want to bookmark this page, and use it instead.

search - Search our database.
  • Genes - Gene search.
  • Phenotypes - Phenotype search.
  • Unigenes - Unigene search.
  • Families - Family search.
  • Markers - Marker search.
  • BACs - BAC (Bacterial Artificial Chromosome) search.
  • Annotations - Full text search of either the manual annotation associated with SGN unigenes, or their BLAST-based automatically assigned annotation.
  • ESTs and libraries - Find EST (Expressed Sequence Tag) libraries by keyword, e.g. library name, organism, tissue, development stage, or authors.
  • Insitu database - A database of in-situ images which can be updated by users, with image add, delete and annotation editing functions. The current images were generated by the floral genome project (FGP). For more information on the floral genome project, visit http://floralgenome.org/ and http://pgn.cornell.edu/.
  • People - Search database of researchers who use SGN.
  • Glossary - Search a glossary of terms used on SGN.
  • Images - Search images contained in the SGN database.
maps - View and compare chromosomes from various organisms.
  • Tomato-EXPEN 2000 - A combined genetic and physical map, showing the association of BACs (Bacterial Artificial Chromosomes) and BAC-Contigs to this genetic map.
  • Tomato physical map - This map is extracted from the S. lycopersicum LA925 x S. pennellii LA716 type F2.2000 genetic map.
  • Tomato contig map - This map shows the positions of the Sanger HindIII/MboI FPC contigs relative to the the S. lycopersicum LA925 x S. pennellii LA716 type F2.2000 genetic map.
  • Tomato IL map - This map shows the locations of the introgressed fragments of S. pennellii in the S. lycopersicum genome, tied to the 1992 map.
  • Tomato FISH map - Map of FISH (Fluorescent In Situ Hybridization) data.
  • Tomato AGP map - The Accessioned Golden Path (AGP) map for the tomato genome.
  • Pepper-AC99 - This map is based on 100 individuals from an inter-specific F2 population of Capsicum. annuum cv. NuMex RNaky and Capsicum chinense var PI159234. 426 molecular markers, including 359 SSR markers 3 specific PCR markers and 68 RFLP markers were used to construct this linkage map, with a total length of 1304.8 cM.
  • Pepper-FA03 - This map is based on 100 individuals from an inter-specific F2 population of Capsicum. annuum cv. NuMex RNaky and Capsicum frutescens BG 2814-6. 728 molecular markers, including 489 SSR markers 195 AFLP, 8 specific PCR markers and 36 RFLP were used to construct this linkage map, with a total length of 1358.7 cM.
  • Potato-TXB 1992 - This is a map based on a S. tuberosum x S. berthaultii BC S. tuberosum population reported in Tanksley et al (1992).
  • Eggplant-LXM 2002 - This map is based on 58 F2 plants from an interspecific cross between S. linnaeanum (MM195) and S. melongena (MM738) and contains 233 RFLP markers.
  • Tobacco SSR 2007 - Nicotiana tabacum
  • Arabidopsis COSII - Arabidopsis thaliana sequenced-based COSII map.
  • Comparative viewer... - Compare chromosomes from different maps, side by side.
  • See all available maps... - All chromosome maps that are available on SGN.
sequencing - Read about sequencing projects.
  • International Tomato Sequencing Project - The gene-rich euchromatic portion of the tomato genome is being sequenced by an international consortium. This page gives more information about the progress of the sequencing effort.
  • Solanaceae project (SOL) - Over the coming decade the International Solanaceae Genome Project (SOL) will create a coordianted network of knowledge about the Solanaceae family aimed at answering two of the most important questions about life and agriculture: How can a common set of genes/proteins give rise to such a wide range of morphologically and ecologically distinct organisms that occupy our planet? How can a deeper understanding of the genetic basis of diversity be harnessed to better meet the needs of society in an environmentally-friendly way? On this page, you will find more information about the strategy that will be used to answer these questions.
  • U.S. tomato sequencing project - An overview of the US Tomato Sequencing Project
  • Browse Tomato Genome Data - Browse tomato genomic sequences and annotations.
tools - Tools for biologists.
  • Sequence Analysis -
  • BLAST - Compare a given sequence to known sequences using the Basic Local Alignment Search Tool, NCBI BLAST v. 2.2.9 [May-01-2004]
  • Alignment Analyzer - Calculate alignments using Muscle v3.6, or view existing alignments using our navigator.
  • Tree Browser - Visualize and manipulate phylogenetic trees from a newick-formatted string.
  • Intron Finder - The SGN Intron Finder works by doing a BLAST search for Arabidopsis thaliana proteins that are similar to the translated protein sequence of the DNA input.
  • Mapping -
  • Comparative Viewer - Compare chromosomes from different maps, side by side.
  • Fast Mapping - A quick mapping program which requires a file in mapmaker format that you can upload.
  • CAPS Designer - Designs CAPS (Cleaved Amplified Polymorphic Sequence) assays for two sequences. Two types of nucleotide inputs are accepted: fasta sequences and clustal aligment. It generates a list of polymorphic enzymes that cut the sequences into different length products.
  • Seed BAC Finder - Lists all anchored BACs for a given chromosome to help identify seed BACs, or suggests a seed BAC given a marker name.
  • Molecular Biology -
  • Primer 3 - Design primers for PCR reactions using several criteria.
  • Signal Peptide Finder - This method of searching for signal sequences is designed to complement SignalP, and has similar success rates.
  • Systems Biology -
  • SolCyc Biochemical Pathways - An interactive map of metabolic pathways.
  • Bulk Query -
  • Unigene and BAC information - Rather than sifting through SGN page by page, here you can download large quantities of information in a single step.
  • FTP Site - FTP (File Transfer Protocol) is more efficient than HTTP (HyperText Transfer Protocol) for transferring large files. Many of our larger archive files are accessible here.
  • ID Converter (SGN <=> TIGR) - The Institute for Genomic Research and SGN maintain independent unigene databases, entries in which tend to have common member ESTs (Expressed Sequence Tags), although they tend not to correspond completely. This tool uses common members to convert back and forth between the two identifier sets.