[Bioperl-l] Intron Exon Retrieval

[Intikhab Alam]

i
 Hi Everybody
I need to retrieve intron exon information, for a list of members, present in a
+protein family. I want to do this task
in commandline interface. Downhere is an email I sent to NCBI, for help.
If somebody have an idea how to retrieve intron exon information, what kind of
+identifiers I need, (I have list of swissprot ids, emble reference and a
+sequence, from swissprot, for every member of protein family of my interest)
+and how I can submit request remotely to NCBI, for intron exon information
+retrieval.
If somebody have an idea, please write me @ intikhab@techfak.uni-bielefeld.de

Cheers


Dear Dr Walker
& Tech Support

Hi

Hope you will be fine.

I am a PhD student, working on some protein families.
I need to retrieve Genomic (Intron / Exon) Structure
(information), for all the members of my protein
families (of interest).

I prefer to do such a task in commandline interface,
rather then web based searches. Becuase in web based
searches, one have to do a long list of members, one
by one, or through a keyword and one may miss some
information. I want to have intron exon information
for members of my protein families, of interest, as
much as possible (existing or defined).

I seen a tool SEALS (Developed by Dr Walker), which
may help me in sequence data retrieval from NCBI. But
I dont know exactly, what identifiers I may use to get
the intron exon information for members of my protein
family of interest. From swissprot, I have curated
Swissprot ID, EMBL reference and the Sequece, for
every member of my protein family of interest. 

Is it possible to retrieve intron exon information, in
commandline interface, for a list of members present
in a protein family, if one have the cross references
for all those members (from Swissprot)??

What kind of identifier I may submit through SEALS (if
possible) for my list of protiens, in commandline
interface to get the intron exon information?

I hope Tech Support or Dr Walker may understand my
problem and help me out to get the this data, for my
future studies.

I will be greatful
and waiting for your reply very soon.

Take Care

Intikhab Alam

http://www.mathematik.uni-bielefeld.de/~intikhab