Question: Finding exon positions from cDNA sequence
0
gravatar for muvinika
4.7 years ago by
muvinika0
muvinika0 wrote:

Hi all,

List some tools to find the position of exons in the cDNA sequence.

Also help me if any package available in R.

sequence R gene • 2.1k views
ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by muvinika0
1

It is not possible to find the exons in cDNA sequence without other information.  What other information do you have or propose to use to get your answer?

ADD REPLYlink written 4.7 years ago by Sean Davis25k

what's your input ?

ADD REPLYlink written 4.7 years ago by Pierre Lindenbaum124k

cDNA sequence

ADD REPLYlink written 4.7 years ago by muvinika0
4

I think I'm going to leave biostars.org

ADD REPLYlink written 4.7 years ago by Pierre Lindenbaum124k

You don't have, just by chance, the genome sequence,too? Just asking.

ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by Dr. Mabuse47k

yes from genome sequence. Sorry i am from computer science so only i could not able to answer clearly.
 

ADD REPLYlink written 4.7 years ago by muvinika0

So, you have cDNA sequence AND the sequence for the chromosomes?  What species are you working with?

ADD REPLYlink written 4.7 years ago by Sean Davis25k

Homosapiens
 

ADD REPLYlink written 4.7 years ago by muvinika0

Rather than creating separate answers, please respond with comments.  

ADD REPLYlink written 4.7 years ago by Sean Davis25k
1
gravatar for Sean Davis
4.7 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

In human, if you have cDNA sequence in FASTA format, you can use BLAT available from UCSC to map your cDNAs against the genome.  The exons will then be the various blocks of the alignments.  

ADD COMMENTlink written 4.7 years ago by Sean Davis25k

thank you

 

ADD REPLYlink written 4.5 years ago by muvinika0

While mapping chromosome to cDNA sequence in BLAT the results are aligned in reverse strand . How do i convert it into forward strand.

ADD REPLYlink written 4.4 years ago by muvinika0
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