Question: Protein Prediction from cancer
0
gravatar for deepakkumarbt
2.6 years ago by
deepakkumarbt0 wrote:

How I can predict all the possible proteins from a cancer genome ??

Please suggest me the way how it can be done.

Cancer Genome (fastq file) -- > preprocessing --> denovo genome assembly -- > protein prediction from assembled genome. ??

sequencing gene assembly genome • 667 views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by deepakkumarbt0
1
gravatar for Satyajeet Khare
2.6 years ago by
Satyajeet Khare1.3k
Pune, India
Satyajeet Khare1.3k wrote:

Protein prediction from cancer genome is difficult. You may need transcriptome (RNA-Seq) for that. From genome, you can get mutations, insertion, deletions and translocations. You may not need de-novo assembly for that. Alignment to existing genome should be sufficient.

ADD COMMENTlink written 2.6 years ago by Satyajeet Khare1.3k
1
gravatar for Nicolas Rosewick
2.6 years ago by
Belgium, Brussels
Nicolas Rosewick7.5k wrote:

One thing you could do is to infer a list of proteins that are modified in cancer genome due to specific mutations leading to modifications in the CDS of transcripts (premature polyA, frameshifts, etc...)

ADD COMMENTlink written 2.6 years ago by Nicolas Rosewick7.5k

Dear Satya & NicoBxl,

Thanks for your response.

I think my question is not clear. Please let me know whether this procedure can be followed or not.

Denovo Assembled Cancer Genome -- > ORF Finders -- > Protein prediction.

I dont want to miss any single protein that can be translated from a cancer genome. My interest is sometimes these proteins may not be of human origin.

Please update me what can be done further.

ADD REPLYlink written 2.6 years ago by deepakkumarbt0

If your ORF finder accurately predicts splicing, you may be able to predict proteins. But its difficult not to "miss any single protein". Since expression of non-canonical ORFs and alternative isoforms is condition specific and may not be predictable from genome sequence.

ADD REPLYlink written 2.6 years ago by Satyajeet Khare1.3k
0
gravatar for deepakkumarbt
2.6 years ago by
deepakkumarbt0 wrote:

Dear Satya & NicoBxl,

Thanks for your response.

I think my question is not clear. Please let me know whether this procedure can be followed or not.

Denovo Assembled Cancer Genome -- > ORF Finders -- > Protein prediction.

I dont want to miss any single protein that can be translated from a cancer genome. My interest is sometimes these proteins may not be of human origin.

Please update me waht can be done further.

ADD COMMENTlink written 2.6 years ago by deepakkumarbt0
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