Bioinformatics Resources and Tools
A database is a structured collection of records stored in a computer system. Genomic databases typically store DNA or protein sequences as well as annotated information about those sequences. Many databases also provide bioinformatics tools tools, such as BLAST, for finding specific sequences or annotations. There are hundreds of genomics databases: some are comprehensive, but are not carefully curated (GenBank), while others are carefully curated, but are narrow (FlyBase).
Bioinformatic tools are computer programs that analyze one or more sequences. There are a dizzying array of bioinformatic tools that can analyze sequences to find protein domains (Pfam), or that can search through databases of millions of sequences to find ones that are similar (BLAST) or that can find potential protein-coding regions (ORF-Finder). Many are freely available over the web. It can be overwhelming to find and use bioinformatic tools because you need to know 1) what type of analysis you wnat performed 2) what type of tool to use 3) where to find the tool.
For this class, we have made a collection of common databases and tools that should be useful for your research. But you should also feel free to use Google to try and find other databases and tools. If you want information on a particular species, you can search for databases that contain DNA sequences for that species (try Medicago truncatula genome). If you want to identify possible functional domains contained within a set of sequences, you can search for annotation tools.
Tools for getting started
NCBI houses sets of databases of sequences for everything under the sun
Searching with BLAST
BLAST known sequences against the Chamaecrista transcriptome
The Chamaecrista genome has not been sequenced. You can explore the transcriptome in a genomics context by taking advantage of the soybean genome since soy is one of Chamaecrista's closer relatives.
The Next Generation Biology Workbench offers a suite of bioinformatics tools. It is convenient "one stop shopping,"
JMP Genomics Tools
JMP Genomics is a statistical software package that lets you look for gene expression patterns. The two links that follow provide the directions and data needed to visualize patterns in gene expression among the different Chamaecrista tissue types. Work through this exercise before you go on to plan your own strategy for working with the expression data. The software is available for all faculty and students in the Biology Department. It is currently on the machines in CMC 109 and the Biology Computer Lab. As a student in the class, you can download your own copy from the COLLAB server folder (Departments/Biology) onto a Windows machine.
JMP Genomics Gene Expression Exercise (Microsoft Word 2007 (.docx) 38kB Feb7 11)
Data File for JMP Genomics Gene Expression Exercise (Text File 5.5MB Jan9 11)
Paper on Analyzing Gene Expression (Acrobat (PDF) 4.7MB Jan11 10) the figures may be helpful as you reflect on the results of your JMP analysis.
Links that will help you relate genes to the biology of organisms:
Plant Ontology is run out of Oregon State University. We have an invitation to help develop a Chamaecrista ontology. If you're interested in thinking about an ontology, you might want to incorporate what you learned in the first two weeks of lab.
Gene Ontology (G0) is focused on what happens at the cell level and below, while Plant Ontology focuses on the level of the cell and above.
Pfam is a database of evolutionarily conserved protein families, and annotations about the functions of those families.
KAAS (KEGG Automatic Annotation Server) provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database and mapping them onto known biochemical/metabolic pathways.
Alignment,Phylogeny, and Evolutionary Analysis Tools:
Clustal Clustal will align multiple DNA or protein sequences. It is available over many different sites, in this case we are providing a link to EMBL's Clustalw server.
CIPRES is a portal for the inference of large phylogenetic trees
: MEGAis a program for constructing alignments and constructing phylogenetic trees. Important:this software does NOT run from the web. You must download it onto a PC and run it locally. The Biology computer lab computers have this software installed on them.
Primer Design Tools
Primer 3 is an excellent tool for designing primers. You will find this helpful in your functional analysis.
Sequence Analysis Tools
There are a number of tools available to analyze sequence data, including 4Peaks, Student Interface to Biology Workbench, and LaserGene. Click here (Microsoft Word 2007 (.docx) 129kB Feb5 10) for detailed instructions on how these programs can be helpful to you.