Chromas Activity

Outcomes for this exercise:

Teacher will be able to read sequence data from an automated sequencer and convert it to a convenient FASTA format text file.

Teacher will be able to correctly edit a FASTA file.

Teacher will be able to submit Fasta file to Blast for a nucleotide-nucleotide search. This is an appropriate first step in looking at sequence data.

 

 

  • You will get a file sent to you by email containing the data from your sequencing run. Save the file to your temporary folder.
  • It is a type of file that can be read by a free software program called Chromas.
  • Download the zip file containing Chromas and save it in your temporary folder. Go to the folder and let the zipfile self-extract. Then open Chromas and load the example file.
  • When we get our real files, Simona will go over the details of using Chromas to fine tune your sequence data. Today we will just learn how to save this data as a FASTA file.

 

 
  • Choose "Edit" ---> "Copy Sequence" ---> "FASTA Format"
  • Then go to "File" ---> "Export"
  • Check that the format is FASTA and give the file a name such as "new_fasta_seq.nuc"
  • Now hide Chromas and open Notepad.
    • You find Notepad by going to "Start" ---> "Programs" ---> "Accessories"
  • Using "Notepad," open the file "new_fasta_seq.nuc" and notice the very important format.

    Line 1:   >The name and information goes here
    Line 2:   HERE IS THE SEQUENCE ONLY, NOTHING ELSE, ESPECIALLY NO EMPTY LINES

Use ctrl-f to find the first "N" and delete it and the rest of the sequence.

Copy and Paste the sequence into nucleotide-nucleotide BLAST! Blast is one of the web-based sequence search engines housed at the National Library of Medicine http://www.ncbi.nlm.nih.gov/.

 
 

 

If you get totally lost, go here.

 

Hopefully your search will return a list of sequences of genes similar to the one you are looking for. If not, your next step will be to find the largest open reading frame, translate it and save the resulting amino acid sequence to a file in the FASTA format and submit that sequence to a BLAST protein-protein search.

last update 7/12/2004