[BiO BB] pls guide me

Iddo Friedberg idoerg at cc.huji.ac.il
Fri Apr 12 07:45:37 EDT 2002

On Thu, 11 Apr 2002, S ET wrote:

: dear members,
: i'm a MSc student from Malaysia. currently i'm working on the L gene
: from Nipah virus.
: i'm a newbie in bioinfomatics, so a would like a ask for an expert to
: guide me personally. well, just to answer me question through
: e-mail....pls???
: for now, i got a situation. the L gene is 6.9k,with no 3D structure
: solved. i need to find out the conserve regions in the gene, what can i
: do?

I would go for Pfam, as a first step.


Find the L-gene product in Expasy (I think there's an entry in TrEMBL
http://www.expasy.org). There is a link provided to Pfam
(http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00946 in your case). Once
the Pfam entry comes up, go to the "Alignment" section, and use JALview
(if you have a Java-enabled browser) to see conserved regions along the
sequence. You can also download various multiple alignment formats for
your own MSA viewer.

This will give you conserved regions within the family. Of course, there
is a plethora of stuff you can do, like finding motifs, etc. You should
consult an expert, a book, or both :) David Mount's `Bioinformatics', and
Arthur Lesk's `Introduction to Bioinformatics' are my favorite
recommendations to people coming into the field from the Biology side.

Damien Counsell did a smashing job in the bioinformatics.org FAQ
(http://bioinformatics.org/faq). Look there too.

As for structure based information: if there is no clear structural
homologue, and you are as you said new to the field, I would not proceed
in that venue without some expert looking over my shoulder.




Iddo Friedberg                                  | Tel: +972-2-6757374
Dept. of Molecular Genetics and Biotechnology   | Fax: +972-2-6757308
The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il
POB 12272, Jerusalem 91120                      |
Israel                                          |

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