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

Wed May 25 10:49:50 UTC 2016

Ok understood, sorry.
Now it works, thank you Andreas.

2016-05-24 20:30 GMT+02:00 Andreas Prlic <andreas at sdsc.edu>:

> 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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