Banner
Image
 Site search  Image Image   ?  Image
Image
  2Can Site Map
Image
NUCLEOTIDE ANALYSIS
Image
 
View Services Site Map
Nucleotide Analysis

 Introduction
 Checking for vector
 contamination

 Blast similarity search
 Fasta similarity search
 Running a whole
genome search

 Pairwise local/global
alignment

 ClustalW multiple
sequence alignment

 Translate DNA/RNA
into protein


Protein and Proteomic Analysis
Protein Function
Protein Structure
Genome Browsing
Database Browsing
Glossary

 
 2can   Nucleotide Analysis
  Checking for vector contamination <<< 2/12 >>>

Running a job with Blast2 EVEC

Using Blast2 EVEC you can now check 2 unknown sequences for contamination. The form for the Blast2 EVEC tool looks as follows:

Go to the main EBI website

  • The sequence is entered into the textbox in fasta format, which consists of a one-line header starting with a ">" symbol, followed by the sequence name. The sequence is then entered on new line(s). You can find out more about sequence formats here.

  • "interactive" is chosen so that I will have the results delivered to the browser as soon as they are available. Alternatively you can chose "email" and fill in your email and have the results delivered via email.

  • The title of the search is left as "Sequence" although you can give your search title any name you wish to help you identify the results.

  • The blastn program is used, which is designed to search a nucleotide query sequence against a DNA databank, in this case the emvec database.

  • The number of scores (hits to the database) and the number of alignments of these against the query sequence to, is left to, in each case 5 to limit the size of the output results.

  • Other options have been left on "default"

  • You now can either go to the Blast2 EVEC page and run the searches yourself or view the sample results for sequence 1 and sequence 2.

  • Which sequence is contaminated?

See an explanation of the results of Blast2 EVEC >>>

<<< Previous || Start of Lesson || Next >>>

2 Can Home Page EBI Home Page