Re: Documentation, tutorials and cookbook about pairwise sequence alignment

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Hi Andrea,

Sorry for the inconvenience. We had to turn the old site off, since there
were too many security breaches which resulted in content spamming. This is
across all bio* projects...

I fixed the links on the CookBook4 page. Checking some of the related
pages, there are still a lot of formatting issues. That will take a bit to
fix them all up. However, each page at the bottom has an "edit this page"
link, which makes it easy to access the raw markdown content.  It is
possible to see the code in a more readable way. I also fixed up this page
for now: http://biojava.org/wikis/BioJava:CookBook3:PSA/

Hope that helps,

Andreas



On Sat, May 21, 2016 at 4:09 AM, Andrea Battistelli <[email protected]
> wrote:

> Hello everyone.
>
> I have been studying the pairwise sequence alignment concept for a project
> that I need to do for an exam.
> In particular I am interested in the global and local alignments and all
> the things related to them (how they are implemented, how I can generate a
> paiwise alignment, ect.).
> I would implement my project in Java employing indeed BioJava as starting
> point.
> I set up correctly the Maven project on Eclipse so no problem under that
> point of view.
>
> Few months ago I have seen there was all the documentation, tutorials and
> specifications about the BioJava project based on the Wiki pages.
> I have seen it has been all migrated into a new web site but now I am not
> finding any documentation, tutorial or cookbook about the topic of personal
> interest.
>
> - In the BioJavaTutorial page - book 2, the alignment module has no pages
> of explanation.
> - In the CookBook4.0, all the links relative to the paiwise sequence
> alignment give me back an "address uninterpretable" message.
> - Finally in the Wiki Pages section there are many links. In some of these
> there are links interesting for me but they contain not well formatted
> codes.
>
> I know that it may taketime to migrate all the things but in the meantime:
> Is there any possibility to have the reference to the old web site?
> Anyone can help me to indicate me where I can find some good pages of
> documentation, tutorial, etc. about pairwise sequence alignment for BioJava?
>
> Thanks a lot.
>
> _______________________________________________
> Biojava-l mailing list  -  [email protected]
> http://mailman.open-bio.org/mailman/listinfo/biojava-l
>



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
RCSB PDB Protein Data Bank
Technical & Scientific Team Lead
University of California, San Diego

Editor Software Section
PLOS Computational Biology

BioJava Project Lead
-----------------------------------------------------------------------

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<div dir=3D"ltr">Hi Andrea,<div><br></div><div>Sorry for the inconvenience.=
 We had to turn the old site off, since there were too many security breach=
es which resulted in content spamming. This is across all bio* projects...<=
/div><div><br></div><div>I fixed the links on the CookBook4 page. Checking =
some of the related pages, there are still a lot of formatting issues. That=
 will take a bit to fix them all up. However, each page at the bottom has a=
n &quot;edit this page&quot; link, which makes it easy to access the raw ma=
rkdown content.=C2=A0 It is possible to see the code in a more readable way=
. I also fixed up this page for now: <a href=3D"http://biojava.org/wikis/Bi=
oJava:CookBook3:PSA/">http://biojava.org/wikis/BioJava:CookBook3:PSA/</a></=
div><div><br></div><div>Hope that helps,</div><div><br></div><div>Andreas<b=
r><div><br></div></div><div><br></div></div><div class=3D"gmail_extra"><br>=
<div class=3D"gmail_quote">On Sat, May 21, 2016 at 4:09 AM, Andrea Battiste=
lli <span dir=3D"ltr">&lt;<a href=3D"mailto:[email protected]" target=
=3D"_blank">[email protected]</a>&gt;</span> wrote:<br><blockquote cl=
ass=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;p=
adding-left:1ex"><div dir=3D"ltr"><div><div><div><div><div><div>Hello every=
one.<br><br></div>I have been studying the pairwise sequence alignment conc=
ept for a project that I need to do for an exam.<br></div><div>In particula=
r I am interested in the global and local alignments and all the things rel=
ated to them (how they are implemented, how I can generate a paiwise alignm=
ent, ect.).<br></div>I would implement my project in Java employing indeed =
BioJava as starting point.<br></div><div>I set up correctly the Maven proje=
ct on Eclipse so no problem under that point of view.<br></div><div><br></d=
iv>Few months ago I have seen there was all the documentation, tutorials an=
d specifications about the BioJava project based on the Wiki pages.<br></di=
v>I have seen it has been all migrated into a new web site but now I am not=
 finding any documentation, tutorial or cookbook about the topic of persona=
l interest.<br><br></div>- In the BioJavaTutorial page - book 2, the alignm=
ent module has no pages of explanation.<br></div><div>- In the CookBook4.0,=
 all the links relative to the paiwise sequence alignment give me back an &=
quot;<span lang=3D"en"><span>address</span> <span>uninterpretable</span></s=
pan>&quot; message.<br></div><div>- Finally in the Wiki Pages section there=
 are many links. In some of these there are links interesting for me but th=
ey contain not well formatted codes.<br><br></div><div>I know that it may t=
aketime to migrate all the things but in the meantime:<br>Is there any poss=
ibility to have the reference to the old web site?<br></div><div>Anyone can=
 help me to indicate me where I can find some good pages of documentation, =
tutorial, etc. about pairwise sequence alignment for BioJava?<br><br></div>=
<div>Thanks a lot.<br></div></div>
<br>_______________________________________________<br>
Biojava-l mailing list=C2=A0 -=C2=A0 <a href=3D"mailto:[email protected]=
en-bio.org">[email protected]</a><br>
<a href=3D"http://mailman.open-bio.org/mailman/listinfo/biojava-l" rel=3D"n=
oreferrer" target=3D"_blank">http://mailman.open-bio.org/mailman/listinfo/b=
iojava-l</a><br></blockquote></div><br><br clear=3D"all"><div><br></div>-- =
<br><div class=3D"gmail_signature"><div dir=3D"ltr"><div><div dir=3D"ltr">-=
----------------------------------------------------------------------<br>D=
r. Andreas Prlic<br>RCSB PDB Protein Data Bank</div><div>Technical &amp; Sc=
ientific Team Lead</div><div dir=3D"ltr">University of California, San Dieg=
o<div><br></div><div>Editor Software Section=C2=A0<br><div>PLOS Computation=
al Biology<div><div><div><br></div><div>BioJava Project Lead<br>-----------=
------------------------------------------------------------<br></div></div=
></div></div></div></div></div></div></div>
</div>

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