[Biopython] BLOCKS BLOSUM

[Iddo Friedberg]

Go here:

http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc232

On Tue, Jun 21, 2011 at 2:01 PM, George Devaniranjan <devaniranjan at gmail.com
> wrote:

> Hi,
> This might not be the correct place to ask this question-but some of you
> may
> have experience in this.
> I went to the BLOCKS database and downloaded a text file that contains many
> BLOCKS but I would like to see the structure of these blocks either in
> VMD/Pymol
> Is there a way to find the PDB ID of these blocks?
>
> What I want is to use the same BLOCKS info and develop my own BLOSUM like
> matrix using biopyhton.
> Thank you and my apologies is this is not directly related to biopython.
> (example of a block from the downloaded text file is given below)
> George
>
> NIF1_AZOCH  (    120)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
> NIF1_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF1_METTL  (    126)  DLDNLFFDVLGDVVCGGFAMPLRDGLAQEIYIVTSGEMMALYAANN
> NIF1_RHISO  (    119)  DIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
> NIF2_AZOCH  (    119)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
> NIF2_CLOPA  (    115)  DLDFVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF2_RHISO  (    119)  DIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
> NIF3_AZOVI  (    118)  DLDFVFFDDLGDVVCGGFAMPIRDGKAQEVYIVASGEMMAIYAANN
> NIF3_CLOPA  (    118)  DLDFVFFDVLGDVVCGGFAMPIRDGKAQEVYIVASGEMMAVYAANN
> NIF4_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF5_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF6_CLOPA  (    115)  DLDFVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIFH_ANASP  (    121)  DLDFVSYDVLGDVVCGGFAMPIREGKAQEIYIVTSGEMMAMYAANN
> NIFH_AZOBR  (    118)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
> NIFH_BRAJA  (    119)  NIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
> NIFH_FRASR  (    116)  NLDFVTYDVLGDVVCGGFAMPIRQGKAQEIYIVTSGEMMAMYAANN
> NIFH_KLEPN  (    118)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
> NIFH_RHILT  (    119)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
> NIFH_RHOCA  (    119)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
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-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html