Internet links on genomics, tools, literature search and other information

Plants, Genes, and Crop Biotechnology, Second Edition by Maarten J. Chrispeels and David E. Sadava.

Techniques, Methods and Tools for DNA Fingerprinting (SNPs, STRs, AFLP) and for Sequencing are available from Beckman Coulter. Download the following Technical Applications Bulletins: AFLP Techniques for DNA Fingerprinting; Precise Microsatellite (STR) Analysis; Multiplex SNP Analysis and Genotyping; Automated Binning for the Generation of Locus Tags; Detecting Heterozygotes; BAC End Sequencing Analysis; CE-based Sequencing: Maximum Read Length at a Minimal Cost (link to be identified). To request the application bulletins go to:http://www.BeckmanCoulterEmail.com/fwp.php?sid=00002_00Na5Gp2x7c0M

DTREE:  A Decision Support System for Safety Assessment of Genetically Modified Crop Plants can be found at http://binas.unido.org/dtreeb   The system is intended to be used as a tool to preserve, disseminate and interpret available data and information regarding releases of genetically modified crop plants into the environment. It is also intended to enhance familiarity with environmental introductions of transgenic crops and provide information support to regulatory authorities, researchers and biosafety officers of public institutions and commercial enterprises.     

Essential Biosafety: The website of Agbios, Canada, on biosafety offers latest scientific and regulatory information for genetically modified crops and foods: www.essentialbiosafety.info

TAIR:  The home page for all of Arabidopsis genomics: has links to genes, maps, markers, proteins, microarrays and many more.  But it’s also a useful resource for all of plant genomics analysis tools such as BLAST, FASTA,  MapViewer, SeqViewer, Chromosome map tool etc. http://www.arabidopsis.org/home.html. TAIR is part of bigger effort by National Genome Resources at http://www.ncgr.org

Gramene:  A comparative mapping resource for grains, rice genomics with info on comparative mapping of rice with other grains; molecular markers and maps http://www.gramene.org/

National Center for Biotechnology Information (NCBI) http://www.ncbi.nlm.nih.gov gets you into Blast and Entrez, Genbank and other databases, genomics tools for data mining, and great literature/journal article searching through PubMed; descriptions of useful books such as Introduction to Genetic Analysis and Modern Genetic Analysis http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed

UK Crop Net: Can link to search databases for barley, millet, cassava, cotton, rice, sorghum and links to useful software http://ukcrop.net/ 

Genoplante: French efforts in genomics; in addition to databases for Arabidopsis, sorghum, wheat and Medicago (model legume) and has links to software programs such as primer design www.genoplante.org

American Society of Plant Biologists has useful links to several aspects of plant biology including plant genomics www.aspb.org   

Plant Genome Data and Information.  Some items of interest include the Plant Genome Database Tutorial; links to crop-specific newsletters http://www.nal.usda.gov/pgdic/

 TIGR Databases: Extensive databases on microbes and parasites; also those resulting from TIGR projects on Arabidopsis, potato and rice http://www.tigr.org/tdb/index.shtml    

Vector DB:  Sequence information for vectors commonly used in molecular biology

http://genome-www2.stanford.edu/vectordb

Plant genomics and agriculture: From model organisms to crops, the role of data mining for gene discovery, an article by V. Mahalkshmi and R. Ortiz. http://www.ejbiotechnology.info/content/vol4/issue3/full/5/

General tools for molecular analysis:   A compilation of internet links to tools for molecular analysis such as DNA/protein sequences searches, sequence alignments, protein structure, finding motifs in proteins, etc.  can be found at http://www.public.iastate.edu/~pedro/research_tools.html

DNA strider program for DNA sequence analysis. If you have a MAC computer, DNA strider is an excellent, user-friendly program for DNA sequence analysis, translation of sequences to proteins, making restriction maps, vector maps.  You can download the DNA Strider from  http://www.personal.psu.edu/faculty/d/s/dsg11/labmanual/Plasmids/Strider_files/DNA_sequence_ files.htm      and there are several URLs that have instructions on how to use it such as http://www.lclark.edu/~bkbaxter/Bio312%20web/strider.htm