Tools

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]

VIGS Tool - Determine which genes a probe will silence using VIGS.

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.


Mapping

Genome Browser (Jbrowse) - browse genomic annotations using the fast Jbrowse browser

Comparative Map Viewer - Compare chromosomes from different maps, side by side.

CAPS Designer - Designs CAPS (Cleaved Amplified Polymorphic Sequence) assays for up to twelve 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.

solQTL: QTL Mapping - A web interface for uploading raw QTL data, on-the-fly QTL mapping, linking predicted QTLs to relevant genetic and genomic data in SGN, and search interface for QTLs.


Molecular Biology

In Silico PCR - In Silico PCR tool based on BLAST

Tomato Expression Atlas (TEA) - The Tomato Expression Atlas

Tomato Expression Database (TED) - The Tomato Expression Database


Systems Biology

SolCyc Biochemical Pathways - An interactive map of metabolic pathways.

Coffee Interactomic Data - Coffee Interactome Data with Cytoscape Web Start viewer.

SGN Ontology Browser - AJAX ontology browser.


Breeder Tools

Breeder Home - Manage a breeding program


Bulk Query

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.

Download Gene Sequences - Download nucleotide or protein sequences for a list of genes

Clones, Arrays, Unigenes and BACs - Rather than sifting through SGN page by page, here you can download large quantities of information in a single step.

Unigene Converter - get the last version of unigenes and tomato gene ids from a list of unigenes.