Bioinformatics question-translate the cDNA sequence into its corresponding protein sequence?

Question

I've translated the cDNA sequence into its corresponding protein sequence

using

ORF Finder (http://www.ncbi.nlm.nih.gov/gorf/go...

the below link shows the result:

http://img217.imageshack.us/img217/...

what kind of information the frames can give to me? which of them I should choose?what they indicate?

Answer 1

Depending on the DNA sequence, the proteins will be shown corresponding to their position within the nucleotide sequence. If you directly started with the protein sequences, all proteins will start at position 0. Beneath the bars representing the proteins, you will find information about exact positions and length of the protein sequence. Within every protein, the colored dashes mark the starting postions of the epitopes predicted by your application.

You should also be able to derive the whole amino acid sequence as well as the epitopes.  Many applications will provide some information on the protein: the number within the DNA sequence (or within your query), the length, the position within the DNA sequence, the reading frame it evolved from, and the number of predicted epitopes for the protein.

ORFs typically can be looked upon as a RNA polymerase and ribosome scanning mechanism; however, no attempt is made to allow for splicing promoters, enhancers, etc. in this version.  The user must define which ORFs are to be associated with the sequence.  You should be able to use additional tools against the protein sequence to dervice additional data:

A hydrophobicity tool will automatically analyze a sequence and produce a graphical representation of the hydrophobicity.



Examine Tool.  This tool allows the user to display detailed information about a sequence.

Display Base or Amino Acid Composition Tool.  If this tool is dropped upon a sequence, the nucleotide or amino acid composition of that sequence is displayed

Align or Match Sequences Tool.  This tool allows the user to perform sequence alignment analysis on sequences.

BLAST Search Tool.  This tool allows the user to search the NIH Databases for sequences related to the sequence the tool is dropped upon.