[Biojava-l] Documentation, tutorials and cookbook about pairwise sequence alignment

[Andrea Battistelli]

Hi Andreas.

Thank you very much for the fixes. Surely it will help me.
I have understood the problem you encountered with the old site.
Now I will try to apply those things.

Thanks again,
Andrea

2016-05-23 19:27 GMT+02:00 Andreas Prlic <andreas at sdsc.edu>:

> 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 <
> andreyas.1688 at gmail.com> 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.
>>
>> _______________________________________________
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>> 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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