help me please

[hazzazi]

[Cat]

I would start with NCBI Blast.

[JackBean]

How will Blast help here?

Seems, like someone's homework, doesn't it? What if you showed us first, what you got already?

[hazzazi]

I try

[Cat]

JackBean, if you Blast this sequence, you will probably find corresponding cDNA and that will help with finding exons in this gene. Alternatively, you can run this sequence (starting with ATG) through translate tool on ExPASy that would give you translation of 1st exon in first reading frame. Then use protein Blast from there to find full protein sequence, cDNA, etc...

And yes, it looks like homework.

[JackBean]

I don't think that's the way he's supposed to do it.

[Cat]

How else would you expect to identify the middle exon?

This looks like bioinformatics problem to me, but Hazzazi is the only one who knows for sure...

[JackBean]

sure it's bioinformatics, but there are other ways, how to determine exon/intron boundaries. How do you think they resolve this after sequenation of new genome?

[Cat]

By comparing DNA data to cDNA data. As far as I know, that is the only foolproof way of determining exon/intron boundaries.

Since this case deals with the actual gene and not a putative one, it would not do to assign probable boundaries based on conserved boundary sequences.

[JackBean]

What do you expect? That the teacher will sequence new species to provide students with brand new sequences?

[Cat]

How do you think they resolve this after sequenation of new genome?

I told you what I think. Can you tell me your answer to this question?

[JackBean]

use bioinformatic tools to identify the exon/intron boundaries. However, I'm not expert in this area of bioinformatics, so I don't know how to do that.