[Genome] Making predicted protein sequence.

[Kayla Smith]

Hello Mahmudul,

Assuming that you're looking at the UCSC Genes track, check the details 
page here:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=knownGene

Step 8 says:

"Protein predictions are generated. For non-RefSeq transcripts we use 
the txCdsPredict program to determine if the transcript is 
protein-coding and if so, the locations of the start and stop codons. 
The program weighs as positive evidence the length of the protein, the 
presence of a Kozak consensus sequence at the start codon, and the 
length of the orthologous predicted protein in other species. As 
negative evidence it considers nonsense-mediated decay and start codons 
in any frame upstream of the predicted start codon. For RefSeq 
transcripts the RefSeq protein prediction is used."

I hope this helps to get you started.  If you have further questions, 
please don't hesitate to contact us again.

Kayla Smith
UCSC Genome Bioinformatics Group

Mahmudul Hasan wrote:
> Hello,
> I am wondering about what method do you use  to make the predicted protein sequence from mRNA or genomic sequence.
>  
> Thanking you,
>  
> Mahmud
> Lund University
> Sweden
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