# Find introns - (May/26/2008 )

Hi,

I have a mRNA position like this:

mRNA join(55349..55526,57779..57881,60486..60721,60934..60968).

I have to find introns and exons from this mRNA position.

I have sequence of length 5621.

I am attaching sequence also.

How do i find introns and exons and display them graphically?

With regards
Archana

-Information-

look into this website, it contains a program called extractseq, you only have to put the coordinates you want to extract, you have to be careful in this tho. the sequence length that you have is 5621, so the coordinate of 55349 would be 1 and 55526 would be 177 and so on.

to display them graphically you can use invitrogen's vector nti if you already have it, if not you can use paint

-toejam-

QUOTE (toejam @ May 27 2008, 12:47 PM)
look into this website, it contains a program called extractseq, you only have to put the coordinates you want to extract, you have to be careful in this tho. the sequence length that you have is 5621, so the coordinate of 55349 would be 1 and 55526 would be 177 and so on.

to display them graphically you can use invitrogen's vector nti if you already have it, if not you can use paint

Hi,

How could u fine that 55349 is 1 & 55526 177 ?

can we translate the sequence?

But can't we do using codes !!!

Any program available?

-Information-

QUOTE (Information @ May 27 2008, 08:02 PM)
Hi,

But can't we do using codes !!!

Any program available?

In an eukaryotic sequence, you can align your mRNA with genomic sequence using simple two sequence alignment, and then manually fine-tune the exon-intron boundaries using GT-AG rule. It works in most cases.
..
Edit: Just in case if you are wondering about GT-AG, see some lectures here: http://search.vadlo.com/b/q?sn=158621799&a...+rule&rel=2
And more on gene prediction: http://search.vadlo.com/b/q?sn=158621799&a...ction&rel=2
..

-cellcounter-

QUOTE (cellcounter @ May 27 2008, 08:24 PM)
QUOTE (Information @ May 27 2008, 08:02 PM)
Hi,

But can't we do using codes !!!

Any program available?

In an eukaryotic sequence, you can align your mRNA with genomic sequence using simple two sequence alignment, and then manually fine-tune the exon-intron boundaries using GT-AG rule. It works in most cases.
..
Edit: Just in case if you are wondering about GT-AG, see some lectures here: http://search.vadlo.com/b/q?sn=158621799&a...+rule&rel=2
And more on gene prediction: http://search.vadlo.com/b/q?sn=158621799&a...ction&rel=2
..

Hi,

Actually i am from programming background?

can i do some program so that i can translate the mRNA part as u did like 1..177?

Any code is available to do that?

-Information-

you can use transeq to translate the mRNA part, there's another program called sixpack to translate. both of these programs belong to the emboss suite.

the way i deduced it was from 1-177 was because of your original coordinates. you have a sequence that is 5621 bp long. that starts somewhere in the base #55349 and ends in #60968. so if you consider that the nucleotide #1 of your 5621 bp long sequence corresponds to 55349 and the last one (5621) to the 60968 nucleotide of the other then you can get any coordenate, e.g. the coordenates you mention in the first post.

the emboss programs have a GUI avaiable at different sites on the internet if you don't have installed it in your computer, just google it by the name and you'll find them. good luck!

-toejam-