help me please

Genetics as it applies to evolution, molecular biology, and medical aspects.

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hazzazi
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help me please

Post by hazzazi » Thu Dec 08, 2011 9:31 pm

:shock:
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Cat
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Post by Cat » Fri Dec 09, 2011 1:33 am

I would start with NCBI Blast.

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JackBean
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Post by JackBean » Fri Dec 09, 2011 7:21 am

How will Blast help here?

Seems, like someone's homework, doesn't it? What if you showed us first, what you got already?
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.

hazzazi
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Post by hazzazi » Fri Dec 09, 2011 7:34 am

I try

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Post by Cat » Sat Dec 10, 2011 1:06 am

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.

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JackBean
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Post by JackBean » Mon Dec 12, 2011 10:35 am

I don't think that's the way he's supposed to do it.
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.

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Post by Cat » Mon Dec 12, 2011 9:09 pm

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...

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JackBean
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Post by JackBean » Fri Dec 16, 2011 1:42 pm

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?
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.

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Post by Cat » Fri Dec 16, 2011 6:15 pm

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.

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JackBean
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Post by JackBean » Sun Dec 18, 2011 10:41 am

What do you expect? That the teacher will sequence new species to provide students with brand new sequences?
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.

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Re:

Post by Cat » Mon Dec 19, 2011 8:28 pm

JackBean wrote: 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?

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JackBean
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Post by JackBean » Tue Dec 20, 2011 12:28 pm

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.
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.

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