[BiO BB] Intron/Exon Analysis

[shashikanth marri]

Hai Oscar Medina,
I have seen your question in bio bulletin board forum.
i would like
give suggestions to your query.
Just by seeing the mRNA sequence we cannot say whether
it is a
alternatively spliced or not if it is a new sequence.
we cannot say
whether it is spliced or not unless we compare it with
 the genomic
DNA.
If you are comparing with the genomic DNA we predict
the exons. the
best tools now avialble online are SIM4
(http://pbil.univ-lyon1.fr/sim4.php) and
SPIDEY
(http://www.ncbi.nih.gov/IEB/Research/Ostell/Spidey/).
wether it is spliced or not we cannot confirm just by
aligning. If any
previous related mRNA are present in that system has
to be known (you
get either from literature search or just do the blast
search and find
related mRNA). which is annotated.

then align your mRNA and annotated mRNA on genomic
sequence and
observe the exon regions. if any exon is missing in
annotated one
compared to the your mRNA then you can say it is
spliced. in other
words your mRNA sequence lies in intronic region of
the annotated mRNA
on genomic DNA then you can say it as spliced form.

If want to do for whole mRNA then take EST sequences
and compare your
mRNA sequence on genomic DNA. then observe any exon
lies on intron
region, or any 5' exonic region extenstion then you
say it as spliced
form.

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