HOW TO BLAST DNA IN NCBI

GENOTYPIC TOOLS SUCH AS GENOME/ SPECIFIC GENE SEQUENCE HOMOLOGY COMPARISON BY BLAST (NCBI AND EMBL)

BLAST

            Basic Local Alignment Search Tool (BLAST) is the tool most frequently used for calculating sequence similarity. BLAST comes in variations for use with different query sequences against different databases. All BLAST applications, as well as information on which BLAST program to use and other help documentation, are listed on the BLAST homepage. This chapter will focus more on how BLAST works, its output, and how both the output and program itself can be further manipulated or customized, rather than on how to use BLAST or interpret BLAST results.

Comparing nucleotide or protein sequences from the same or different organisms is a very powerful tool in molecular biology. By finding similarities between sequences, scientists can infer the function of newly sequenced genes, predict new members of gene families, and explore evolutionary relationships. Now that whole genomes are being sequenced, sequence similarity searching can be used to predict the location and function of protein-coding and transcription-regulation regions in genomic DNA

NCBI

            The National Centre for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is located in Bethesda, Maryland, and was founded in 1988 through legislation sponsored by US Congressman Claude Pepper.

The NCBI houses a series of databases relevant to biotechnology and biomedicine and is an important resource for bioinformatics tools and services. Major databases include GenBank for DNA sequences and PubMed, a bibliographic database for biomedical literature. Other databases include the NCBI Epigenomics database. All these databases are available online through the Entrez search engine. NCBI was directed by David Lipman, one of the original authors of the BLAST sequence alignment program and a widely respected figure in bioinformatics.

NCBI had responsible for making available the GenBank DNA sequence database since 1992. GenBank coordinates with individual laboratories and other sequence databases, such as those of the European Molecular Biology Laboratory (EMBL) and the DNA Data Bank of Japan (DDBJ)

EMBL

            The European Molecular Biology Laboratory (EMBL) is an intergovernmental organization dedicated to molecular biology research and is supported by 28 member states, one prospect state, and one associate member state. EMBL was created in 1974 and is funded by public research money from its member states. Research at EMBL is conducted by approximately 110 independent research and service groups and teams covering the spectrum of molecular biology and bioinformatics. The list of Groups and Teams at EMBL can be found at www.embl.org. The Laboratory operates from six sites: the main laboratory in Heidelberg, and sites in Hinxton (the European Bioinformatics Institute (EBI), in England), Grenoble (France), Hamburg (Germany), Rome (Italy) and Barcelona (Spain). EMBL groups and laboratories perform basic research in molecular biology and molecular medicine as well as train scientists, students, and visitors. The organization aids in the development of services, new instruments and methods, and technology in its member states. Israel is the only full member state located outside Europe.

STEPS INVOLVED IN BLAST

1.      Going to the NCBI/EMBL website, you will see a number of options. Choose a species to search, or you can compare your sample against all the species in the database.

2.      You will need to decide on a BLAST program

3.      To search nucleotides against nucleotides, select “blast” or “megaBLAST” (this second category is considered the fastest).

4.       To search proteins against proteins, select “blastp”

5.      “blastx” will do the opposite of blast, searching a translated nucleotide database with your protein query

6.      All “tBlast” search translated nucleotide database with your translated nucleotide query.

7.      Once you have decided which BLAST program to use it’s very easy and web- based just copy and paste your sequence into the right area and fill out few other areas per instructions (each program is a little different, but easy to follow)