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

Tue May 24 18:30:02 UTC 2016

Hi Andreas,

please don't mail me directly with questions, but keep them on the list,
for the benefit of other users who might be in the same situation.

You are right, the signature of SubstitutionMatrix has changed at some
point in the past. Try this:

SubstitutionMatrix<AminoAcidCompound> matrix =
SubstitutionMatrixHelper.getBlosum65();

There is also another example in the "demo" package of the alignment
module, that you could take a look at.

About the tutorial: When you have the basics figured out, any
contributions/pull requests to improve the tutorial will be welcome!
;-)

A

On Tue, May 24, 2016 at 5:51 AM, Andrea Battistelli <andreyas.1688 at gmail.com
> wrote:

> Hi Andreas.
>
> I have seen the codes in the page you suggested me.
> I have encountered some errors about:
>
> *import org.biojava.nbio.alignment.template.SequencePair;*
>
>
> *import org.biojava.nbio.alignment.template.SubstitutionMatrix;*
> Regarding all the other imports, there are not problems.
> Indeed in the code I have errors in this part:
>
> *SubstitutionMatrix<AminoAcidCompound> matrix = new
> SimpleSubstitutionMatrix<AminoAcidCompound>();*
> *List<SequencePair<ProteinSequence, AminoAcidCompound>> alig =
> Alignments.getAllPairsAlignments(lst,*
> *                PairwiseSequenceAlignerType.LOCAL, new
> SimpleGapPenalty(), matrix);*
> *for (SequencePair<ProteinSequence, AminoAcidCompound> pair : alig) {*
> *            System.out.printf("%n%s vs %s%n%s",
> pair.getQuery().getAccession(), pair.getTarget().getAccession(), pair);*
> *}*
> It is told me to create these two classes.
>
> I am using the last version of the BioJava project (4.2.1) by means of
> Maven (as described in the site).
> Probably in that version there are not anymore those classes*. *Could be
> this the problem?
> How could I solve this?
>
> Thanks a lot.
>
> P.S.
> Regarding the "BioJavaTutorial page - book 2: The Alignment module" (
> https://github.com/biojava/biojava-tutorial/blob/master/alignment/README.md),
> could be possible kindly to have the explanation of the pages?
> Unfortunaltely it is the onyl part of the tutorial without explanation.
>
>
> 2016-05-24 14:12 GMT+02:00 Andrea Battistelli <andreyas.1688 at gmail.com>:
>
>> 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.
>>>>
>>>> _______________________________________________
>>>> Biojava-l mailing list  -  Biojava-l at mailman.open-bio.org
>>>> 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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