Finding exon positions from cDNA sequence

Question

[muvinika]

Hi all,

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

Also help me if any package available in R.

[Sean Davis]

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?

[Pierre Lindenbaum]

what's your input ?

[muvinika]

cDNA sequence

[Pierre Lindenbaum]

I think I'm going to leave biostars.org

[Michael]

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

[muvinika]

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

[Sean Davis]

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

[muvinika]

Homo sapiens

[Sean Davis]

Rather than creating separate answers, please respond with comments.

Answer 1

[Sean Davis]

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.

[muvinika]

Thank you

[muvinika]

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