For Bio-synthetic gene cluster analysis, many tools required protein input sequence that's why we have to submit protein sequence for analysis of putative gene clusters.
That's a purely programming task that may be easily accomplished with Perl or Python.
You may find scripts and lots of knowledge at www.rosalind.info
But my hat's off to this brilliant, succint solution for RNA in Python from a user called Gorysko
from Bio.Seq import Seq
from Bio.Alphabet import generic_rna
file = open("RNAseq.txt", "r")
rna = Seq(file.read(),generic_rna)
protein = rna.translate()
print protein
Hope it helps...
Hello.
as Mr Baro told you: perfect task for python.
Your question does not give further details, so please also think about the following:
you spoke of WGS data ... be sure that you use a database where coding sequences (CDS) are provided. (Todays WGS projects will provide it, otherwise it's not published in a good journal. But if you told a company to do a whole genome sequencing for your own very special organism, annotation may be not included in the basic offer. [It costs of hundereds of hours of work of a specialized bioinformatician to do it for a new organism with unknown genome properties]).
Creating proteins from genomic sequences will cause senseless results because of introns and other non-translated regions, as you might imagine.
Regards, J
well jorg i am quite agree with you that Creating proteins from genomic sequences will cause senseless results because of introns and other non-translated regions, here i want to annotate actinobacterial WGS for putative biosynthetic gene clusters... only for this i have require protein sequences as input file.
You can provide your nucleic acid sequences directly to antiSMASH to predict biosynthetic gene clusters.
http://antismash.secondarymetabolites.org/
try this
https://bip.weizmann.ac.il/education/materials/gcg/tfasta.html
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Cell Biology
- Culture Cells
- Cell Line