[BiO BB] How can I retrieve the biggest transposableelementfromNCBI?

Mike Marchywka mmarchywka at eyewonder.com
Sun May 7 10:59:52 EDT 2006



The reason I was so enthusiastic is I had been meaning to do this for
a while as I had a backlog of proteins I wanted to compare and contrast.
This, and the recent set of more basic links posted over the last few days
got me to the point of making the needed additions to my scripts. In paricular,
manual selection by size is important to avoid precursors, stupid fragments,
variants, etc.

The link from Dan Bolser pointed me to a bunch of uniformly coded ranking systems
http://www.expasy.org/cgi-bin/protscale.pl?Q7U3V6
that I could parse with another script. Getting the text color modules from CPAN,
I now have a pretty easy way to compare/color code just the proteins I want with
clustalw. So, I get things like this in color:

$ more cd28comp.aln |proteinparse -tr aa/dolittle
Table loaded ok
CLUSTAL       W
AAA51944      -MLRLLLALNLFPSIQVTGNKILVKQSPMLVAYDNAVNLSCKYSYNLFSREFRASLHKGL
AAK37601      -MLRLLLALNLLPSIRVTGNKILVKQSPMLVAYDNAVNLSCKYSYNLFSREFRASLHKGL
AAK37604      -MLRLLLVLNLFPSIQATGIKILVKQSPMLEAYDNTVNLTCKYSCNLFSRQFQASLHKGV
CAA63707      -MLRLLLALNFFPSIQVAENKILVKQSPMLVVNDNEVNLSCKYTYNLFSKEFRASLYKGA
BAA92349      MILRLLLALNFFPSIQVTENKILVKQLPRLVVYNNEVNLSCKYTHNLFSKEFRASLYKGV
AAB53574      MILRLLLALNFFPSIQVTENKILVKQLPRLVVYNNEVNLSCKYTHNFFSKEFRASLYKGV
AAF72533      MILRLLLALNFFPSIQVTENKILVKQLPRLVVYNNEVNLSCKYTYNLFSKEFRASLYKGV
CAA39003      MTLRLLFLALSFFSVQVTENKILVKQSPLLVVDNNEVSLSCRYSYNLLAKEFRASLYKGV

Anyone have comments on bioperl? This seems to keep coming up in google
as I look for modules to install. I keep building my own stuff and have a pretty
big collection of works in progress ( kluges). There are probably canned packages
that do these things better.

FWIW, I anticipate looking at things like the following:
1) Immune signalling- the immediate interest is tgn1412 ( comes up on google) 
and species translation issues when dealing with immune pathways ( cd28 and ctla-4 in the
present case). 
2) If I ever get back to it, an earlier interest in defective ribosomes/translation and immunotherapy.
That is, Dendreon had one paper claiming that frame shifted proteins were unique to 
and may be general features of cancers ( animal data on an immunotherapy targeting a
frame shifted protein looked pretty compelling). 
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15568617&query_hl=7&itool=pubmed_docsum

You can appreciate the needs here- finding candidate alternative-reading frame peptides
that can be observed by the immune system suggests that you may want to try speculative translation schemes applied to genome sequences and then feed to epitope prediction stuff etc.
Or, look at published peptides and see what mis-translated genes they may derive from. 

3) General issues in translating animal results into people as they may be described
in small differences in key proteins- AA sequence and postranslational modifications.

4) Data mining from scientific abstracts- nothing particularly novel here but
I have been amazed at how easy it is to overlook simple search strategies until
a script output some phrases/ideas. 



-----Original Message-----
From: bio_bulletin_board-bounces+mmarchywka=eyewonder.com at bioinformatics.org [mailto:bio_bulletin_board-bounces+mmarchywka=eyewonder.com at bioinformatics.org]On Behalf Of zheng hui
Sent: WednesdayMay-03-2006 11:08 AM
To: bio_bulletin_board at bioinformatics.org
Subject: RE: [BiO BB] How can I retrieve the biggest transposableelementfromNCBI?


Thank you for your enthusiastic help.  I have some exprience in perl 
programing but don't know eUtils before.  This tool is a real powerful 
utility and I feel so glad that you introduce it to me.




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